Federal research funding to tackle areas like cancer, diabetes and heart disease is lagging by about $1 billion behind the levels of recent years, reflecting the chaotic start of the Trump administration and the dictates that froze an array of grants, meetings and communications.

The slowdown in awards from the National Institutes of Health has been occurring while a legal challenge plays out over the administration’s sudden policy change last week to slash payments for administrative and facilities costs related to medical research. A federal judge in Massachusetts has temporarily blocked the cutbacks, pending hearings later this month.

Federally funded research has driven major advances in cutting-edge gene therapies and immune-system-boosting treatments for certain cancers, cystic fibrosis and sickle cell disease.

The broader lag in funding is being felt at universities and medical centers from Baton Rouge to Boston, according to congressional lawmakers who are tracking it. Federal spending records show the allocations are about $1 billion lower than last year’s disbursements were at this time.

N.I.H. funding has ground to a halt in the past 10 days, according to Senator Tammy Baldwin, Democrat of Wisconsin.

“The president has completely stopped funding for research that discovers cures for diseases that devastate families across the country, like cancer and Alzheimer’s disease, all so he can give tax breaks to billionaires and big corporations,” Ms. Baldwin said in a statement on Friday. “Make no mistake, their efforts to rob Peter to pay Paul means crushing families’ hopes and dreams of having cures.”

It was not clear whether the stalled funding reflected an administrative backlog or efforts by Trump officials to defy the rulings of judges who have temporarily quashed efforts to freeze federal grant-making and spending.

In the first six weeks of 2024, the N.I.H. awarded more than 11,000 grants amounting to roughly $2.5 billion. During the same time period this year, the agency doled out about $1.4 billion, a figure hundreds of millions of dollars lower than the amount awarded within this period for the last six years. The agency issued about $36 billion in grants last year.

Some administration officials have criticized the research grants, saying they reflect a liberal bias and are dedicated to diversity and equity efforts. Some critics also contend that certain universities receive far larger outlays to cover overhead costs than other institutions.

A spokeswoman for the N.I.H. did not immediately return a request for comment.

Earlier this week, Senator Patty Murray, Democrat of Washington, tried to add a provision to a budget bill that would have restored the N.I.H. funding to agreed-upon levels. The effort failed on a party-line vote.

“Trump and Elon — either through sheer ignorance or a genuine lack of caring — are putting lifesaving research in America on life support,” she said in a statement, referring to the billionaire Elon Musk.

The N.I.H. has undergone considerable turmoil in recent days, with two high-ranking officials announcing sudden departures. The agency has no permanent leader in place yet, though Jay Bhattacharya, the Trump administration nominee and a Stanford professor, has begun to make the rounds in Congress as his confirmation hearings approach.

Robert F. Kennedy Jr., the secretary of the top federal health agency, has said he wants to back off on infectious disease research, a core N.I.H. study area, and focus instead on chronic diseases, which the agency also studies. The agency has 27 separate institutes and centers that fund studies and develop treatments for diseases like cancer and heart conditions as well as infectious diseases like AIDS and Covid.

Meetings at the agency — during which experts review grant applications and make funding recommendations — were abruptly canceled at the end of January after the new administration issued a sweeping communications ban, effectively halting the funding of new research. Some of those meetings have since resumed. The White House budget office also ordered a pause on all federal grants, which it rescinded days later.

The proposed cuts to indirect costs to medical research alone have been enough to raise deep concerns at Dartmouth and at other institutions.

“If the federal government cuts its investment, we will have to scale back on research, and cutting-edge science will be cut short,” Dean Madden, the vice provost for research at Dartmouth’s medical school, said at a news conference on Friday. “You don’t know what discoveries won’t be made as a result, but they might include a cure for some childhood cancer or treatment for Alzheimer’s or dozens of other diseases that are afflicting patients across our country.”

A Texas county is taking steps to declare a state of emergency and seek federal assistance over farmland contaminated with harmful “forever chemicals,” as concerns grow over the safety of fertilizer made from sewage.

Johnson County, south of Fort Worth, has been roiled since county investigators found high levels of chemicals called PFAS, or per- and polyfluoroalkyl substances, at two cattle ranches in the county in 2023.

The county says the PFAS, also known as forever chemicals because they don’t break down in the environment, came from contaminated fertilizer used on a neighboring farm. That fertilizer was made out of treated sewage from Fort Worth’s wastewater treatment plant. A New York Times investigation into the use of contaminated sewage sludge as fertilizer focused in part on the experience of ranchers in Johnson County.

PFAS, which is used in everyday items like nonstick cookware and stain-resistant carpets, has been found to increase the risk of certain types of cancer, and can cause birth defects, developmental delays in children, and other health harms.

County commissioners passed a resolution this week calling on Texas governor Greg Abbott to join the declaration, and seek federal disaster assistance.

“This is uncharted territory,” said Larry Woolley, one of the county’s four commissioners, in an interview. The funds, he said, would be put toward testing and monitoring of drinking water, cleanup, as well as euthanization of cattle contaminated from the soil, crops and water.

Johnson county is also pressing the state of Texas to block the use of sewage sludge to fertilize local farmland. “Ultimately, our goal is to stop the flow of contaminants into the county,” said Christopher Boedeker, a county Judge.

For decades, farmers nationwide have been encouraged by the federal government to use treated sewage sludge as fertilizer for its rich nutrients, and to reduce the amount of sludge that must be buried in landfills or incinerated. Spreading sewage on farmland also cuts down on the use of fertilizers made from fossil fuels.

But a growing body of research shows that the black sludge, made from the sewage that flows from homes and factories, can contain heavy concentrations of PFAS as well as other harmful contaminants.

Last month, under the Biden administration, the Environmental Protection Agency for the first time warned that PFAS-tainted sewage sludge used as fertilizer can contaminate the soil, groundwater, crops and livestock, posing human health risks.

The Biden administration also set drinking-water standards for certain kinds of PFAS and designated two of the chemicals as hazardous substances that must be cleaned up under the nation’s Superfund law. The future of those measures is uncertain under the Trump administration. The E.P.A. says there is no safe level of exposure to those two PFAS.

There has been little testing on farms. Maine is the only state that has started to systematically test farmland for PFAS, and has shuttered dozens of dairy farms found with contamination.

Johnson County is the first to directly seek federal assistance. It remained unclear, however, exactly how the county could tap federal funds, particularly amid the Trump administration’s freeze on federal spending.

President Biden’s Bipartisan Infrastructure Law had provided $2 billion in funding to address PFAS and other contaminants in drinking water. It is the future of funds like these, which must be requested at the state level, that remain uncertain in the new administration.

The Federal Emergency Management Agency also has funds available for well testing, which must be requested by states, though that money is typically distributed after natural disasters. President Trump has also targeted FEMA funding, saying he wants states to handle disasters without the federal agency’s help. The Department of Agriculture also offers assistance to farmers affected by PFAS contamination, but that program is currently limited to dairy farmers.

That leaves Johnson County in a bind.

While President Trump has been hostile to regulations, he also spoke on the campaign trail of “getting dangerous chemicals out of our environment.” And concerns about PFAS contamination have reached some deeply red states and counties, like Johnson County, which voted overwhelmingly for Mr. Trump.

The E.P.A. and FEMA did not provide comment.

In December, Texas attorney general Ken Paxton sued the largest PFAS makers, saying they knew about the dangers of these chemicals, but continued to market their use. The G.O.P.-controlled Texas state legislature is considering bills that set limits on PFAS in sludge fertilizer and require producers to test for the chemicals.

The state of Texas has not indicated whether they will back Johnson County’s declaration and support its request for federal assistance. The governor’s office did not respond to requests for comment.

Ricky Richter, a spokesman at the state’s environmental regulator, the Texas Commission of Environmental Quality, said the agency’s own analysis of PFAS levels discovered by Johnson County investigators did not suggest any harm to human health or the environment.

The agency did not immediately provide details of its analysis.

Johnson county officials said they stood behind their findings. The ranchers are suing the fertilizer provider, alleging that the contamination on their land was slowly sickening and killing their livestock. They are still caring for the surviving cattle, but are no longer sending them to market.