The report, released by the Institute of Medicine's (IOM) committee, found that the FDA currently couldn't ensure the safety of new prescription drugs because of inadequate funds, structural problems, and unclear and insufficient regulatory authorities.
The FDA said that while it appreciated the findings of the committee's report, it pointed out that much progress and reform of its safety oversight enterprise was already under way.
"The agency in recent months had improved efforts to ensure the safety of new prescription drugs through a number of measures," said Andrew von Eschenbach, the FDA's acting commissioner.
"For example, FDA is developing new tools for communicating safety information to patients."
Others within the FDA were quick to flaunt the steps the agency's already taken.
"We're simply saying we have been on a trajectory to address the issues," said Janet Woodcock, the FDA's deputy commissioner for operations.
But Sheila Burke, chair of the IOM committee, called much of the effort little more than "moving boxes" around on organisational charts.
"They have not been an integrative solution. They have addressed pieces of it but not in a fulsome way," she said.
In its controversial report, the committee said that the FDA needed 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, and came up with a series of recommendations to improve safety review.
At present, once a drug is approved in terms of safety, it's very difficult for the regulator to withdraw it from the market, unless major evidence shows the drug's risks for patients.
These problems in FDA regulative authority were highlighted when the popular painkiller Vioxx, manufactured by Merck, was pulled from the market in 2004, five years after its approval, because long-term use was linked to an increased risk of heart attack and stroke.
Responding to the report, von Eschenbach admitted: "While considerable work has been done over the past two years to improve our approach to drug safety, work still remains to be done."
"I'm committed to taking additional steps and will look to the initiatives recommended by the Institute of Medicine to ensure we continue to fulfil our mission."