For the first time, the Environmental Protection Agency has warned that “forever chemicals” present in sewage sludge that is used as fertilizer can pose human health risks, saying in a study on Tuesday that, in some cases, the risks could exceed the agency’s safety thresholds “sometimes by several orders of magnitude.” The agency maintained, however, that the general food supply was not at risk.

A growing body of research has shown that the sludge can be contaminated with manmade chemicals known as per- and polyfluoroalkyl substances, or PFAS, which are used widely in everyday items like nonstick cookware and stain-resistant carpets. The chemicals, which are linked to a range of illnesses including an increased risk of cancer, do not break down in the environment, and, when tainted sludge is used as fertilizer on farmland, it can contaminate the soil, groundwater, crops and livestock.

Last year, The New York Times reported that 3M, which for decades has manufactured PFAS, found as early as 2000 that the chemicals were turning up in sludge samples from municipal wastewater plants across the country. In 2003, 3M told E.P.A. of its findings.

The E.P.A. has for decades encouraged the use of sludge from treated wastewater as inexpensive fertilizer with no limits on how much PFAS it can contain. But the agency’s new draft risk assessment sets a potential new course. If finalized, it could mark what could be the first step toward regulating PFAS in the sludge used as fertilizer, which the industry calls biosolids. The agency currently regulates certain heavy metals and pathogens in sewage sludge used as fertilizer, but not PFAS.

The Biden administration has tackled PFAS contamination elsewhere, setting limits on PFAS in drinking water for the first time and designating two kinds of PFAS as hazardous under the nation’s Superfund cleanup law. Those rules came after the agency said in 2023 that there is no safe level of exposure to those two PFAS.

The new E.P.A. assessment “provides important information to help inform future actions by federal and state agencies,” as well as sewage treatment plants and farmers, “to protect people from PFAS exposure,” Jane Nishida, the E.P.A. acting administrator, said in a statement.

It’s unclear what further steps the incoming Trump administration might take. President-elect Trump has been hostile to regulations; however, he spoke on the campaign trail of “getting dangerous chemicals out of our environment,” and concerns about PFAS contamination in fertilizer have reached some deeply red states.

The E.P.A.’s risk study comes as farmers across the country have been discovering PFAS on their land.

In Maine, the first and only state that is systematically testing its farmland for PFAS, dozens of dairy farms have been found to be contaminated. In Texas, a group of ranchers sued the provider of sludge fertilizer last year after a neighboring farm used the fertilizer on its fields. County investigators found several types of PFAS in the ranchers’ soil, water, crops and livestock, and the ranchers have since sued the E.P.A., accusing the agency of failing to regulate PFAS in biosolids. In Michigan, state officials shut down a farm where tests found particularly high concentrations in the soil and in cattle that grazed on the land.

The E.P.A. said its analysis did not suggest the general food supply was at risk. Sewage sludge is applied to less than 1 percent of the fertilized acreage of agricultural land a year, it said, a number that roughly aligns with industry data. And, not all farms where sewage fertilizer was used would present a risk.

Still, studies have found that, because PFAS is so persistent in the environment, tainted sludge applied years or even decades ago can continue to be a source of contamination. More than 2 million dry tons were used on 4.6 million acres of farmland in 2018, according to the biosolids industry. Farmers have obtained permits to use sewage sludge on nearly 70 million acres, or about a fifth of all U.S. agricultural land, the industry said.

The E.P.A. hasn’t changed its policy of promoting sludge fertilizer, which has benefits along with the risks. It is rich in nutrients, and spreading it on fields cuts down on the need to incinerate it or put it in landfills, which would have other environmental costs. Using sludge fertilizer also reduces the use of synthetic fertilizers that are based on fossil fuels.

The agency said in its new assessment that at farms that used contaminated sludge, the highest human risks involved drinking milk from pasture-raised cows raised on a contaminated farm, from drinking contaminated water, from eating eggs from pasture-raised hens or beef from cattle raised on contaminated land, or from eating fish from lakes and ponds contaminated with runoff.

Particularly at risk were households that live near or relied on products from a contaminated source, for example milk or beef from a family farm contaminated with PFAS from sewage sludge, the agency said. It said in certain conditions, risks exceeded the E.P.A.’s acceptable thresholds by several orders of magnitude.

The general public, which is more likely to buy milk from a grocery store that sources its produce from many farms, was at less risk, the agency said. For its assessment, the E.P.A. focused on the two most commonly detected types of forever chemicals, called PFOA and PFOS, though many others exist.

The Food and Drug Administration does not set limits on PFAS levels in food. Since 2019, however, the agency has tested nearly 1,300 samples and said the vast majority were free of the types of PFAS the agency is able to test for.

Some public health experts and advocacy groups have questioned the testing methodology, and the agency itself says that “PFAS exposure from food is an emerging area of science and there remains much we do not yet know.” Last year, Consumer Reports said it had detected PFAS in some milk, including organic brands. Packaging is another source of PFAS in food.

The National Association of Clean Water Agencies, which represents wastewater treatment plants across the country, said the findings reinforced that sludge fertilizer was not a risk to the public food supply. Sludge providers have argued that they should not be held responsible for PFAS contamination, saying the chemicals are simply passed onto them.

“Ultimately, the manufacturers of these chemicals must bear the responsibility and cost to remove these chemicals” from their products and environment, said Adam Krantz, the group’s chief executive.

In the absence of federal action, states have started to take their own measures. Maine banned the use of sewage sludge on agricultural fields in 2022 and remains the only state to have done so. In December, a Texas lawmaker introduced a bill that would place limits on levels of certain kinds of PFAS in sewage sludge applied to farmland. Oklahoma lawmakers have also introduced a bill that would place a moratorium on the use of sludge on farmland.

An outright ban on the use of sludge as fertilizer would bring its own problems. Wastewater sludge still needs somewhere to go. Since Maine’s ban, some wastewater treatment plants say they have been forced to ship sewage sludge out of state.

Environmental experts say what’s important is limiting the amount of PFAS that ends up in wastewater and sewage in the first place. That could come from phasing out the use of PFAS in everyday products, or requiring manufacturers to treat polluted wastewater before sending it to municipal wastewater treatment plants.

Israel and Hamas are engaging in another round of talks in Qatar on Tuesday as they near an agreement for a cease-fire in Gaza and the release of hostages, according to a diplomat and a Palestinian in touch with Hamas leaders.

The new talks were a sign that the negotiations, mediated by Qatar, Egypt and the United States, were making progress after months of failed attempts to achieve a breakthrough.

If Hamas and Israel conclude a deal, it would bring some respite to Palestinians in Gaza, who have endured miserable conditions in displacement camps and relentless bombardments by Israel, and for the families of hostages abducted from Israel, who have worried for more than a year about the fate of their loved ones.

The diplomat said the talks would focus on addressing outstanding issues, while the Palestinian said they would center on details of how to implement an agreement.

Both the diplomat and the Palestinian spoke on condition of anonymity to discuss sensitive diplomacy.

Past rounds of talks have seen hopes rise only to be dashed days later, with Israel and Hamas each blaming the other for the impasse.

The emerging agreement, the diplomat said, was heavily inspired by previous proposals discussed in May and July.

The Americans were not happy.

The migrant situation at the border was out of control, they said, and Mexico was not doing enough to stop it, according to officials from both countries.

In fact, the crisis was worse than Mexican officials had been led to believe by their own immigration chief, Francisco Garduño Yáñez.

The revelation in October 2023 led Mexico’s defense secretary at the time to fly into a rage at an emergency meeting, officials with knowledge of the encounter said.

“You fooled me,” the defense secretary, Luis Cresencio Sandoval González, yelled at Mr. Garduño, according to two people familiar with the incident.

The defense secretary regularly briefed Mexico’s then-president, Andrés Manuel López Obrador. But, Mr. Sandoval had learned days earlier from the Americans that the migrant crisis was more dire than he realized.

“You hid information from me, making me lie to the president,” the defense secretary lashed out.

It was a tense chapter in U.S.-Mexico relations, according to five Mexican and American officials privy to bilateral talks on migration, and Mr. Garduño, 76, had landed in the middle of it. Beyond being accused of mismanaging and minimizing the migrant crisis, he is separately facing criminal charges in connection with a fire at a migration detention center that killed 40 people in 2023.

Now, as Mexico stands on the precipice of what are expected to be contentious border discussions with the incoming Trump administration, the same Mexican official blamed for mismanaging the migrant crisis, Mr. Garduño, will be a pivotal player in those negotiations. The American president-elect has vowed to begin mass deportations of undocumented immigrants as soon as he takes office.

The Defense Ministry, Mr. Garduño and the agency he led, the National Migration Institute, did not respond to several requests for comment.

Controlling the Mexico-U.S. border is a sprawling endeavor, involving thousands of government agents from both countries. The issue is often used as a political cudgel. U.S. House Republicans accused the Biden administration of failing to control the border and voted to impeach his homeland security secretary, Alejandro Mayorkas.

In Mexico, Mr. Garduño was the one in the cross hairs.

A former director of Mexico’s prison system, he has been criticized for relying on troops to help manage migrant flows. Mr. Garduño’s agency has also been accused of essentially waving migrants through to the northern border for bribes. In interviews, migrants said they had to pay Mexican migration agents to travel through the country to reach the United States.

In 2022, the British Embassy also commissioned a classified report on Mexico’s migration system, a copy of which was obtained by The New York Times. It found systemic corruption in the government’s handling of migrants, including extortion, sexual abuse and collusion with criminal organizations to kidnap migrants for ransom.

In a 2022 interview, Mr. Garduño defended his performance, saying he had fired nearly half of the agency’s employees for extorting migrants. His agency had issued documents to nearly two million migrants from 2018 to 2022, he said, helping to regularize their presence in the country.

It is “a humanitarian policy of integration and brotherhood,” he said.

But interviews with officials from both countries have laid bare the discontent of American officials with how Mexico was handling migration.

In 2023, President Biden’s popularity was slipping ahead of the 2024 elections. Migration was a top concern among American voters. So the president dispatched Secretary of State Antony J. Blinken and Mr. Mayorkas for an emergency meeting in Mexico City that October.

They told Mr. López Obrador that American border agents had encountered nearly 220,000 migrants at the southern U.S. border that September — one of the largest flows ever recorded, officials with knowledge of the meeting said.

Border patrol agents were overwhelmed. The freight trains from Mexico to the United States had no security. Corrupt conductors, the Americans said, were stopping or slowing the trains to allow migrants to hop on.

They asked Mexican officials to move more aggressively to break up large groups of migrants heading to the U.S. border and to end visa-free travel for countries whose nationals used Mexico to enter America illegally, officials said.

The reality that the American delegation revealed was grimmer than the one presented by Mr. Garduño’s agency, which gave daily briefings to the Mexican administration on the number of migrants intercepted in southern Mexico.

Three officials working on migration and were privy to those figures said the numbers rarely correlated with the data presented by the U.S. Customs and Border Protection and the government of Panama, which many migrants pass through to reach Mexico.

The Mexican military reported that it and the migration agency encountered five million migrants from 2018 to 2024, but Mexico’s Interior Ministry reported about half that number in that time. The 2023 numbers varied widely as well; the migration agency reported nearly 1.5 million encounters that year, whereas the Interior Ministry reported about 500,000.

“Mexico’s government is blurring the picture by issuing two widely divergent numbers, without even explaining the divergence,” said Adam Isacson, a director at the Washington Office on Latin America, a research institute. “It’s confusing, it undermines the government’s credibility, and it makes it harder to anticipate emerging trends.”

After the U.S. delegation returned to Washington, Mr. López Obrador called the emergency meeting of Mexico’s most senior security and migration officials on Oct. 13, 2023. It was held in Tapachula, a city on the border with Guatemala and a funnel for migrants entering Mexico.

The city’s refugee agency was about to collapse, with about 7,000 migrants a day flooding its offices to register as asylum seekers — a fast track to receiving a migrant permit.

The permits were sort of a golden ticket: They allow asylum seekers to study, work and get access to basic services. Though asylum seekers are supposed to stay in the state where they apply, many use the Mexican permits to navigate to the U.S. border without being detained, officials say.

At the emergency meeting, the interior secretary at the time, Luisa María Alcalde Luján, zeroed in on the permits, officials said.

She grilled Mr. Garduño about whether his agency was handing out the permits but allowing asylum seekers to head north toward the U.S. border, according to four officials with knowledge of the meeting, two in attendance.

Yes, Mr. Garduño replied.

As Ms. Alcalde berated him, Mr. Garduño looked down at his lap and fell silent, officials with knowledge of the encounter said.

She then announced to the room that she was stripping Mr. Garduño of the ability to hand out new migration permits without the approval of other government branches.

Ms. Alcalde did not respond to requests for comment.

As soon as the migrant permits stopped, thousands of asylum seekers in Mexico were plunged into legal limbo.

The move made them “easier prey for criminal groups,” said Dana Graber Ladek, the Mexico chief of mission for the International Organization for Migration. It left “migrants with basically no option to be able to work legally in the country,” she added.

Eventually, Mexico restarted issuing the migration permits, but today they are a trickle of what they once were: Only about 3,500 permits were issued last year, compared with nearly 130,000 in 2023.

After the meeting, Mr. Garduño quickly moved to demonstrate that his agency was capable of controlling migrant flows, officials said.

His agents made it harder for migrants to reach the U.S. border and stepped up security on the trains many used to travel north. The number of migrants encountered at the U.S.-Mexican border dropped from September to November by nearly 13 percent, according to November 2023 statistics from the U.S. Customs and Border Protection.

But just as the numbers trended down, a leak prompted high-level officials to call another emergency migration meeting in Mexico.

The Mexican treasury secretary temporarily stopped funding parts of the government in November 2023, including Mr. Garduño’s agency, because of budgetary constraints. But instead of lobbying the treasury to release funds, as other officials did, Mr. Garduño proactively halted his agency’s operations.

On Dec. 1, he sent a memo ordering his agency to pause deportation flights that carry undocumented migrants, withdraw personnel from checkpoints and shut down the busing program that had relieved pressure on the northern border.

The memo was swiftly leaked and went public.

Migrants rushed to the U.S. border, many unhindered by Mexican migration agents. That December, U.S. Customs and Border Protection registered the highest number of migrant encounters on the border in history: nearly 250,000 migrants.

Overwhelmed American border patrol agents shut land border crossings in Lukeville, Ariz., and San Diego. The U.S. border protection agency suspended several railway crossings in Texas.

Mexico’s government, trying to contain the fallout, publicly pledged more funds to its migration agency. Mr. Blinken flew back to Mexico City, on Dec. 27 — with an even larger delegation.

The next month, January 2024, after Mexico and the United States cooperated to enforce stricter measures, the migrant flow at the U.S. border was cut in half.

The pressure from Washington has continued to work; unlawful border crossings have declined. Last June, Mr. Biden issued an executive order to essentially block undocumented migrants from receiving asylum at the border.

Mexico has deployed National Guard troops to immigration checkpoints and bused migrants farther south, exhausting their efforts to head north. The authorities have also broken up migrant caravans so they no longer reach the U.S. border.

In October, Claudia Sheinbaum was sworn in as president of Mexico. She named a new immigration chief, but said Mr. Garduño would continue to advise the government to create a “profound transformation” of its migration agency and to help weather the storm after Mr. Trump takes office Jan. 20.

Mr. Garduño still faces criminal proceedings over the migration center fire. Several Mexican and American officials said they thought he would resign after the tragedy. But he has been a confidante of Mr. López Obrador for decades.

Mr. Garduño is not under arrest, but every two weeks, he must check in with the prosecuting judge.

Emiliano Rodríguez Mega and Paulina Villegas contributed reporting.