Every five years, top officials of the Food and Drug Administration go behind closed doors to negotiate the terms of the agency's core budget.

The F.D.A. isn't at the table with members of Congress. It is in dozens of meetings with representatives of pharmaceutical companies. Drug, device and biotech companies make payments to the agency in order to get product approvals. Nearly half of the F.D.A.'s budget is financed by the fees, which have soared since the program's inception.

Three-quarters of the agency's drug division budget was spent on the pharmaceutical industry last year.

Congress is debating the details of the program as a deadline looms. The pharmaceutical lobby says it has helped speed approvals of drugs by giving it the resources to do the work. The industry has been able to weaken the approval process for drugs because of the agreements.

Dr. Joseph Ross is a professor at the Yale School of Medicine and has studied F.D.A. policies.

An effort to speed approval of generic drugs that could cut into the big companies' profits and make the drugs less expensive for consumers and insurers was included in the user fee bill. The major pharmaceutical lobby opposed that provision.

The House and Senate have versions of the bills that include proposals to increase oversight of cosmetics, diagnostic tests, and food packaging.

Drug and device industries spend hundreds of millions of dollars on lobbying and campaign contributions and those measures may not survive final haggling over reauthorizing the program. The amendment that would allow the F.D.A. to help generic drug makers replicate an off-patent drug with specifics on the ingredients was opposed by Senator Richard Burr.

The generic drug measure could save taxpayers $546 million over the next decade. Mr. Burr voted against the bill in June because he thought it would hamper innovation. The stripped down user fee bill was introduced in July.

ImageRichard Burr, in a dark suit with a yellow and blue striped tie and dark-rimmed glasses, arrives at the top of an escalator.
Senator Richard Burr of North Carolina, a leading member of the Senate committee that oversees the F.D.A., voted against a user fee bill in June.Credit...Al Drago for The New York Times
Richard Burr, in a dark suit with a yellow and blue striped tie and dark-rimmed glasses, arrives at the top of an escalator.

The Senate committee that oversees the F.D.A. is chaired by Senator Patty Murray of Washington.

She said she was laser focused on patients and making sure F.D.A. works for families. The F.D.A. can't be forced to send out pink slips. We can't and won't stop pushing for reforms from the drug industry and this agency.

The user fee program was discussed in committee hearings.

The F.D.A.'s drug division has a significant role to play in funding and furthering policy goals of the organization, which is why the pharmaceutical companies have a tendency to charge outrageously high prices.

The Senate Health, Education, Labor & Pensions Committee held a hearing on June 14th. I don't think it makes sense to me.

The program burdens companies with negotiating with the agency over the fees, which Mr. Burr predicted would go up even more. The high costs of the program limit the opportunities for small businesses.

In a perfect world, he said, he would like to see no user fees paid to the F.D.A. The agency's priorities are decided by the White House and Congress.

The program was not ideal according to the F.D.A. commissioner. He said that he wished the taxpayer paid for all the F.D.A.

The F.D.A. policy does not allow officials to comment on pending legislation.

AIDS activists pressed the F.D.A. to speed up drug approvals. About a decade later, drugs moved through the system more quickly with an average of about 10 months.

The program's funding grew over time. The F.D.A. tries to make quick decisions, hold regular meetings with drug companies and approve products under fast-track pathways.

Medical devices, generic drugs and biologics have user fees added to them. The tobacco division and its 1,200 employees are funded entirely by user fees and the industry has no say in how the dollars are spent. Drug companies made up half of the F.D.A. drug division's budget by the year 2000.

ImageRobert Califf sits in a dark-paneled Senate hearing room before a microphone, wearing a white-and-purple bow tie and a light purple shirt under a tan jacket.
“Philosophically, I wish the taxpayer paid for all the F.D.A. and there weren’t user fees,” said Dr. Robert Califf, the F.D.A. commissioner.Credit...Anna Rose Layden for The New York Times
Robert Califf sits in a dark-paneled Senate hearing room before a microphone, wearing a white-and-purple bow tie and a light purple shirt under a tan jacket.

According to Dr. Mitchell, the fee program's policy changes Favored industry through decreasing regulatory standards, shortening approval times and increasing industry involvement in F.D.A.

The number of clinical trials for drug approval was reduced from two to one in 1997 because of user fee negotiations. The 2012 user fee law allowed smaller or shorter clinical trials for therapies for life threatening conditions.

The quicker you rush to approval, the more likely you are to miss something that could hurt patients.

Highly controversial F.D.A. drug approvals have been made. Medicare refused to pay for the Alzheimer's drug Aduhelm because it didn't have enough evidence of benefit. Another approval of a medication for a deadly muscle disease drew scrutiny when insurers wouldn't pay for it. The agency gave those approvals if further study proves a benefit, which takes years to complete.

The F.D.A. said the user fee process gave it the authority to improve public health by expanding oversight of foreign drugmakers and allowing hearing aids to be sold over the counter.

The F.D.A.'s drug approval process was changed by the user fee process.

There are many people with us today who would not be here if it weren't for the program.

The program's value in ensuring the F.D.A. has the staff and technology to review a growing number of rapidly changing gene and cell therapies, novel medical devices and rare has been noted by those testifying. The funding made the F.D.A. a global leader in approving three-fourths of new medicines before any other nation, according to the pharmaceutical research manufacturers of America.

The growth of the program reflects the robust innovation and timely access to safe and effective medicines needed for an appropriately staffed and funded F.D.A., according to a statement.

Scott Whitaker is the president of AdvaMed, which represents medical device makers.

ImageA portrait of Reshma Ramachandran shows her standing on green grass against a background cast in shadow late on a summer day, wearing a light blue t-shirt and dark blue pants, her hands clasped in front of her.
Dr. Reshma Ramachandran, a professor of medicine at Yale University, said doctors often don’t recognize the pressure the drug industry exerts over the F.D.A.Credit...Christopher Capozziello for The New York Times
A portrait of Reshma Ramachandran shows her standing on green grass against a background cast in shadow late on a summer day, wearing a light blue t-shirt and dark blue pants, her hands clasped in front of her.

Sanket Dhruva is an assistant professor of medicine at the University of California, San Francisco. He recently encountered a cardiac device that was approved after a study followed patients for only 30 days. He didn't have enough information to use the device on the patients he was treating.

He said that doctors could make more money by adopting the newest technologies and that hospitals liked to advertise them, though clear evidence of safety and effectiveness wasn't always present.

Dr. Dhruva said that the hype was what ended up going on.

F.D.A. guidance has deemed unethical the practice of testing new cancer drugs against placebos instead of against standard therapies. He doesn't know if the new drugs are better than the old ones.

Doctors weren't trained to look through F.D.A. records to scrutinize the quality of the studies that led to approvals. Many people don't know that the drug industry exerts pressure on the F.D.A.

The wrong metric to care about is the user fee process, according to a doctor who tracks it. Patients should be asked if they are healthier. Is patient safety a priority? That seems to be an unimportant thing.

There were about 100 meetings between the F.D.A. and drug companies and six meetings with groups.

Concerns that the drug and device industries hold outsize sway compared with patient groups and public-interest advocates have led to calls for Congress to find a way to fully fund the agency.

According to a former F.D.A. adviser, the F.D.A. should match its fast pace of approvals with a system that could.

The F.D.A. doesn't have a good way to monitor the side effects of drugs once they're on the market. It is not as good as it should be to ensure the safety of the public.