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.”