Last week, the FDA's deputy commissioner Scott Gottlieb said that pharma companies should contribute additional funds so the agency can study the drugs' safety once they reach the market.
The US drug industry is now negotiating the fourth version of the Prescription Drug User Fee Act (PDUFA) with the regulator - the outcome could change radically the landscape for pharma companies.
Until now, user fees paid by firms have primarily been used to review the safety and efficacy of new drugs before they are approved to be sold on the market.
However, during a speech at the Manhattan Institute last week, Gottlieb recommended to increase fees in order to hire extra staff to monitor pharmaceuticals once they are marketed.
The Pharmaceutical Research and Manufacturers of America, the industry's trade association which represents US leading pharmaceutical and biotech companies, refused to comment until the negotiations have concluded but stressed that the fee formula - which allows to calculate the fees - was among the features of the bill endorsed by the industry, and that it continues to support it.
Drugmakers began paying fees to the agency in 1992 in a bid to get a faster drug review system under PDUFA.
Since then, PDUFA has been renewed three times and the third iteration expires in October next year.
What was supposed to be only supplemental now represents more than half of the budget for drug review and in 2007, the FDA is expected to collect more than $86m (€67m) in new drug user fees.
However, it is important to put things into context and note that the European equivalent of the FDA, the EMEA, has three quarters of its budget based on industry fees and the UK's drug approval body is entirely funded by pharma companies.
Meanwhile a source close to the FDA told In-PharmaTechnologist.com that while boosting fees to increase the FDA's post-approval supervisory functions was a good intention, it would not change the fact that the pharma industry has a powerful voice and it will keep putting pressure on the regulator.
"PDUFA is a very attractive thing for pharma companies as it allows the FDA to speed up the drug review process," the source said.
"It has been renewed until now not because it is good, but because it is convenient for the industry."
The source added that it didn't mean that the FDA's drug safety system would be improved but the FDA would be more economically pressured by drug firms.
A single drug now takes over $1.2bn to develop due to the complexity and duration of the trials required, added to the need to comply with strict regulations, and the industry will be happy to pay more if it allows to speed up things but only if companies get to define the conditions, according to the source.
Drug safety concerns intensified after Merck pulled arthritis pill Vioxx from the market two years ago when a study showed long-term use doubled the risk of heart attack and stroke.
In addition, a report on the FDA's drug approval process by the Institute of Medicine (IOM) published in September said that the agency needs more budget and manpower to ensure it keeps its focus on the safety of the drugs it regulates, not only before approval, but also throughout the time they are on the market.
"We found an imbalance in the regulatory attention and resources available before and after drug approval," said at the time Sheila Burke, deputy secretary and chief operating officer of the Smithsonian Institution and chair of the committee.
"Staff and resources devoted to preapproval functions are substantially greater. Few high-quality studies are conducted after approval."
The FDA admitted that more needed to be done to ensure the safe and effective use of prescription drugs, however it pointed out that much progress and reform of its safety oversight enterprise was already under way.