Senior Food and Drug Administration officials were told that the application to sell the "morning-after pill" without prescription was going to be rejected before the staff completed its scientific review and months before the decision was made public, government investigators reported yesterday.

A report by the independent Government Accountability Office also said senior FDA officials, including then-Commissioner Mark B. McClellan, were actively involved in the politically sensitive decision -- one of four aspects of the agency's actions that the investigators called "unusual."

The GAO report, requested by Congress more than 16 months ago, said the agency did not follow its normal procedures in making the scientific assessment of the Plan B proposal and in having a top official sign off on the eventual decision after lower-ranking scientists refused.

Critics of the FDA's handling of the issue said the report confirmed their view that the agency had allowed politics to trump science. The application was strongly opposed by some social and religious conservatives, including 49 members of Congress who wrote a letter to President Bush asking that the application be rejected.

The FDA, in a statement responding to the report, said: "We question the integrity of the investigative process that results in such partial conclusions by the GAO. The report mischaracterizes facts and does not appear to take into consideration the input provided by the FDA."

But Susan F. Wood, a former FDA assistant commissioner for women's health who left her job to protest the agency's actions, said: "This report is a sad reminder of why I felt compelled to resign. Instead of improving and advancing women's health, the FDA leadership is ignoring its process and not relying on science and medical evidence."

The GAO report said then-Commissioner McClellan raised numerous objections to the proposal for over-the-counter sales of Plan B in a staff meeting three months before it was rejected.

The report also said that McClellan, who left the FDA two months before the rejection was announced to run the Centers for Medicare and Medicaid Services, did not respond to written questions from the GAO except to say that he left before the decision was made and that his actions had been "consistent with his usual practices."

In a letter to Health and Human Services Secretary Mike Leavitt, Reps. Henry A. Waxman (D-Calif.) and John D. Dingell (D-Mich.) said the GAO was unable to fully assess McClellan's role because he would not speak with investigators and because the agency provided no documents reflecting his communications with other officials. The FDA told the investigators that e-mails to and from McClellan had been deleted and that written memos were routinely destroyed.

Raising the possibility that this practice was a violation of federal record-keeping law, the congressmen wrote that "as the Plan B decision makes clear, retaining the documents of the agency head is essential for the transparent operation of government."

Plan B, manufactured by Barr Laboratories, is an emergency contraceptive that can prevent pregnancy if taken within 72 hours of unprotected sex. The drug was approved by the FDA in 1999 as a prescription medication, but advocates say the time needed to get a doctor's appointment and prescription often makes emergency contraception far less effective.

Critics of the Plan B decision have charged that the decision was made in the White House, which was under pressure from conservative activists who believe over-the-counter availability of Plan B would promote teenage promiscuity. Some also believe Plan B causes abortions, although the FDA considers it to be a contraceptive.

GAO investigator Marcia Crosse said the GAO did not look into White House involvement. The investigation "specifically did not look at interactions outside of the FDA -- with the White House or HHS," she said. "That is not part of what we agreed to review."

The GAO report also found significant discrepancies in what lower- and higher-ranking FDA officials recalled about the process.

The report said, for instance, that the leaders of some FDA science divisions and offices recalled that top officials, including Steven Galson and Deputy Commissioner for Operations Janet Woodcock, told them months before the rejection that the application would not be approved. Woodcock and Galson, then acting director of the Center for Drug Evaluation and Research, recalled that they only discussed the possibility of a rejection and what might be missing from the application. It was Galson who signed the Plan B rejection in May 2004 after the lower-ranking officials who would normally have signed off refused.

In a formal response to the report, Woodcock said the agency followed normal procedures for a controversial drug application.

The report led some lawmakers, including Rep. Louise M. Slaughter (D-N.Y.), to call for hearings. "This report is the 'smoking gun' which clearly demonstrates that the FDA based its decision on politics, and not science," she said.

But Wendy Wright, executive vice president of Concerned Women for America, said the GAO report showed that the FDA had made the correct decision. "Making Plan B over the counter would needlessly expose adolescents to risks and reduce access to health care to those in need of it," she said.

A subsequent application to make Plan B available over the counter only to women older than 17 was also indefinitely postponed by the FDA in August. At the time, then-Commissioner Lester M. Crawford said it was unclear whether the agency had the legal authority to make a drug available without prescription only to older women.

Crawford was reported earlier to have declined to speak to the GAO investigators. The GAO report said that although he did not respond before leaving his job in September, his attorney subsequently sent a written statement saying that Crawford played no role in the first Plan B review.

Susan Wood, former FDA assistant commissioner, said the GAO report reminds her of why she resigned.Mark McClellan, FDA's then-commissioner, weighed in on the Plan B decision, the GAO said.