When federal drug officials suspected in 1992 that a popular allergy pill might cause heart problems, they turned to their own scientists. Their trial confirmed the danger, and the drug was pulled from the market.

Eight years later, similar worries surrounded the arthritis pill Vioxx. But by then, the Food and Drug Administration had shifted gears, slashing its laboratories and network of independent drug safety experts in favor of hiring more people to approve drugs - changes that arose under an unusual agreement that has left the agency increasingly reliant on and bound by drug company money. Discovering Vioxx’s dangers would take four more years.

That delay has led to a firestorm of criticism. Members of Congress, an internal F.D.A. whistleblower and prominent medical journals have said that the agency is incapable of uncovering the perils of drugs that have been approved and are in wide distribution. Some have accused it of being cozy with drug makers.

Dozens of former and current F.D.A. officials, outside scientists and advocates for patients say that the agency’s efforts to monitor the ill effects of drugs that are on the market are a shadow of what they should be because the White House and Congress forced a marriage between the agency and industry years ago for the rich dowry that industry offered.

Under the 1992 agreement, the industry pledged to give the agency millions - in the 2003 fiscal year, $200 million - but only if the agency spent a specified level of money on new drug approvals.

As Congressional support sank since then, the agency has cut everything else but new drug reviews. In the past 11 years, spending on the reviews has increased to more than four-fifths of the agency drug center’s budget from about half.

Among the priorities that took the worst hit was ensuring the safety of the drugs that patients are already taking. Drug companies test their products in people before they are approved, but sometimes potentially serious problems arise only when they are being used by millions of people. The F.D.A. has never been able to require drug makers to undertake new safety tests once a drug is approved, so tracking the safety of drugs already on the market is the agency’s responsibility.

But as a result of the agency shifting its resources, almost everyone, including critics, outside drug safety experts, medical journal editors, some industry executives and even top agency officials, now agrees that its mechanisms for uncovering the dangers of drugs after they have been approved are woefully inadequate, particularly, as was the case of Vioxx, when the potentially damaging side effect is not an unusual ailment.

The F.D.A.‘s present safety monitoring system “is not good for determining if a drug increases the rate of a side effect already common in the population,” said Dr. Janet Woodcock, acting deputy commissioner for operations at the agency.

Indeed, the agency now relies almost entirely on the willingness of drug makers to report problems that crop up after a drug has been approved to ensure the safety of the nation’s drug supply. Some critics say that this dependency has gradually worn away at the agency’s willingness to confront drug makers, making it timid and leaving patients vulnerable.

“This is not just about dollars,” said Dr. Jerry Avorn, a professor at Harvard Medical School and the author of “Powerful Medicines.” “It’s a cultural issue in which the agency feels it can’t pressure drug makers.”

Now lawmakers are considering proposals for a center for drug safety that would be independent of the agency’s new drug reviewers. The departing health and human services secretary, Tommy G. Thompson, said Friday that he favored creating such a center. After initially opposing the idea, agency officials have said that they will study any proposals.

These proposals may not have been needed if not for the details of the 1992 agreement, which began with the best of intentions. AIDS, cancer, heart disease - all were terrible diseases that drug makers’ laboratories were confronting. But their remedies were languishing for years on F.D.A. shelves because the agency did not have the money to hire enough reviewers.