Funding cuts to the National Institutes of Health and the U.S. Food and Drug Administration could sharply reduce the number of new drugs available to Americans in the coming decades, according to an analysis released on Friday by the Congressional Budget Office.

The Trump administration has proposed shrinking the budget of the N.I.H., the world’s premier funder of medical research, by $18 billion, or nearly 40 percent. But even a 10 percent reduction would prevent roughly 30 additional drugs from coming to market in the next three decades, the budget office said.

The budget office also assessed a hypothetical scenario in which staffing reductions at the F.D.A. would delay the review of new drugs by nine months. Such delays would prevent 23 additional drugs from becoming available in that time period, according to the analysis.

About 3,500 F.D.A. workers, roughly 15 percent of the work force, have been laid off by the Trump administration or have left voluntarily in recent months.

The cuts come at a time of rapid innovation in gene therapies and in targeting rare diseases, cancers and mental health disorders, said Rena Conti, who directs the Technology Policy and Research Institute at Boston University. “Having these type of cuts will fundamentally set back progress in meeting the demand for these type of therapies,” she said. “And that leaves patients without hope.”

The budget office issued its assessment in response to a request from several members of Congress opposed to the cuts, including Senator Jeff Merkley, Democrat of Oregon. This group provided the office with the scenarios it ended up assessing, including the hypothetical nine-month delay to drug reviews.

It is unclear how budgets at the federal health agency will ultimately change under President Trump. The administration’s proposed 40 percent cut to N.I.H. has faced criticism from key members of Congress, including Republicans.

Dr. Marty Makary, the F.D.A. commissioner, has insisted to Congress that the staffing cuts have not affected the timeline for approving new drugs. But employees at the agency have blamed delays in some new drug approvals on staffing shortages and greater workloads.

A spokesman for the Department of Health and Human Services, which oversees both the N.I.H. and the F.D.A., said in response to questions about the C.B.O. analysis on Friday: “The solution isn’t always more money — for us it’s smarter policy.”

Under Health Secretary Robert F. Kennedy Jr., the spokesman said, the health department was “focused on doing more with less by cutting red tape, streamlining drug reviews, and making sure every taxpayer dollar delivers real results to improve our nation’s health.”

The budget office focused on the effect of a 10 percent cut to the money that the N.I.H. distributes to universities and medical centers for the medical research that precedes clinical trials. By the third decade after such a cut, when its impact on drug development would be fully felt, 20 fewer drugs would come to market each decade, a reduction of 4.5 percent, the budget office said..

In the Trump administration budget proposal, external N.I.H. spending designated for universities and other research institutions is expected to be reduced by more than 40 percent, from nearly $27 billion in 2025 to about $15 billion, reflecting the overall proposed cut, according to a Senate staff member.

Cuts to other N.I.H. funding channels, including the money that the agency directs to clinical trials, would further reduce new drug availability, the budget office found.

“It seems to me that the lost drugs are more likely to be the novel ‘first in class’ drugs that have the potential to substantially change health care and improve the lives of patients,” said Jeremy M. Berg, a former director of the National Institute of General Medical Sciences at the N.I.H.

The budget office said that an increase in review times at the F.D.A. would delay drug approvals and increase the cost of developing new drugs. By the second decade after such a delay took effect, the budget office said, the increase in review times would be associated with 10 fewer new drugs each decade, a 2 percent reduction.

The F.D.A. has approved 25 new drugs so far this year, and in a typical year it authorizes about 60 new drugs, according to data compiled by Citeline, a pharmaceutical market consulting company. The budget office built its analysis on a more conservative estimate that about 44 drugs would be approved per year.

The Trump administration has also slashed funding for medical research by terminating or delaying grant awards, without congressional approval. (Federal judges have since declared some of those cuts illegal.)

Nearly every drug that has come to market in the United States in recent years has emerged at least in part from federally funded medical research. Of the 356 drugs approved by the F.D.A. from 2010 to 2019, 354 benefited in part from N.I.H. funding, one study found.

Weight loss drugs like Ozempic sprang from early research funded by the N.I.H. Medications approved in the last decade have drastically improved survival rates and quality of life for people with cystic fibrosis, some blood cancers and melanoma, a type of skin cancer.

Many drugs fail in early trials, and the pharmaceutical industry often will not spend its money on the type of foundational research the N.I.H. funds, in part because the payoffs are so unpredictable.

“The United States leads the world in medical innovation because of our continued investments in research and development at the N.I.H.,” the lawmakers who requested the budget office analysis said in a statement. In addition to Mr. Merkley, the group included Sen. Bernie Sanders of Vermont and two Democratic representatives, Frank Pallone, Jr., of New Jersey and Brendan F. Boyle of Pennsylvania.

“This unprecedented assault on our health care institutions by the Trump administration will cut off access to medicines that patients are waiting for, and cause wide-ranging harms to our nation’s economy,” they said.

Members of Mr. Trump’s party, too, have criticized the proposed N.I.H. cuts. Senator Susan Collins of Maine, a Republican who chairs a key appropriations committee, has called the proposed N.I.H. reduction “so disturbing” and warned that “it would delay or stop effective treatments and cures.”