The Government Accountability Office, a nonpartisan investigative arm of Congress, concluded in a report released Monday that the Food and Drug Administration's May 2004 rejection of the morning-after pill, or emergency contraceptive, application was unusual in several respects.

Top agency officials were deeply involved in the decision, which was "very, very rare," a top F.D.A. review official told investigators. The officials' decision to ignore the recommendation of an independent advisory committee as well as the agency's own scientific review staff was unprecedented, the report found. And a top official's "novel" rationale for rejecting the application contradicted past agency practices, it concluded.

The pill, called Plan B, is a flashpoint in the debate over abortion, in part because some abortion opponents consider the pill tantamount to ending a pregnancy. In scientific reviews, the F.D.A. has concluded that it is a contraceptive.

The report suggested that it quickly became apparent that the agency was not going to follow its usual path when it came to the pill. "For example," it said, "F.D.A. review staff told us that they were told early in the review process that the decision would be made by high-level management."

Top agency officials denied many of the report's findings, including its conclusion that the top officials' involvement was unusual and that they had decided to reject the application before the agency's own scientific review was concluded. Julie Zawisza, an F.D.A. spokeswoman, said the agency stood by its rejection of the morning-after pill application.

"We question the integrity of the investigative process that results in such partial conclusions by the G.A.O.," Ms. Zawisza said.

Earlier this month, after Senator Patty Murray, Democrat of Washington, denounced the agency's decisions on the pill, Health and Human Services Secretary Michael O. Leavitt also said the agency had acted appropriately.

But on Monday, Dr. Susan F. Wood, former director of the agency's office of women's health, said that what she described as the F.D.A.'s willingness to ignore science in the service of abortion politics has "only gotten worse" since the events that were the focus of the G.A.O. investigation. Dr. Wood resigned in August after the agency decided to delay its decision on the morning-after pill once again.

Senator Murray and Senator Hillary Rodham Clinton, Democrat of New York, issued a statement saying that the report "has confirmed what we have always suspected, that this was a politically motivated decision that came down from the highest levels at the F.D.A."

The investigation was requested by 30 House members and 17 senators. On Monday, 18 Democratic House members signed a letter of protest to Mr. Leavitt.

The letter noted that Congressional investigators had been unable to uncover the role in the Plan B decision played by the former agency commissioner, Dr. Mark B. McClellan, because agency officials told investigators that all of his e-mail messages and written correspondence on the subject had been deleted or thrown out. The Democrats charged that these acts contravened federal records laws.

Planned Parenthood Federation of America, the nation's largest provider of abortion services, issued a statement saying, "The G.A.O. report confirms the F.D.A. has been playing politics with women's health all along."

Wendy Wright, executive vice president of Concerned Women for America, a conservative women's advocacy group in Washington, said that the report's finding that top agency officials had overruled staffers was comforting. "The F.D.A. has been making some pretty serious mistakes lately," Ms. Wright said.

Plan B is manufactured by Barr Laboratories and is now available only with a prescription. Manufacturers rarely criticize the F.D.A., fearing that doing so might anger agency officials. Carol Cox, a Barr spokeswoman, chose her words carefully.

"While we're disappointed that the F.D.A. has not approved Plan B for over-the-counter use, we continue to seek that approval," Ms. Cox said.

Plan B was originally manufactured by Women's Capital Corporation, which won approval from the F.D.A. in 1999 to sell the drug by prescription. The pill contains high doses of the medicines present in birth control pills.

If taken within 72 hours of unprotected sex, Plan B generally prevents pregnancy. But it is most effective taken soon after sex, prompting the efforts to make it available quickly and without a prescription.

In April 2003, Women's Capital applied to make Plan B available over the counter. Barr bought the rights to the drug and continued to pursue the application. An advisory committed voted 23 to 4 in December 2003 to recommend approving the switch.

Within days of the committee's vote, however, Dr. Janet Woodcock, the F.D.A.'s acting deputy commissioner of operations, and Dr. Steven Galson, acting director of its drug center, told four top staff members that the application would be rejected, even though the agency's scientific review of the application had yet to be completed, the staff members told Congressional investigators. That review was completed in April.

Drs. Woodcock and Galson denied to investigators that they had made such statements.

Dr. Galson told them that "although he was '90 percent sure' as early as January 2004" that he would reject the application, he made his final decision only after reviewing the scientific evidence.

From 1994 to 2004, F.D.A. advisory committees reviewed 23 applications to switch drugs from prescription to over-the-counter status. Plan B was the only one of those 23 in which the agency went against the committee's advice.

Dr. Galson said in a May 2004 news conference that while he had consulted other top officials at the agency, the decision to reject the Plan B application was his alone. He decided to issue a "non-approvable" letter to Barr, he said, because only 29 of 585 participants in a Barr study of the drug had been ages 14 to 16. None was under 14.

Dr. Galson said younger teenagers might act differently than older ones and might engage in riskier sex if they knew an emergency contraceptive was easily available. The company needed more data to ensure that this was not true, he said.

But the G.A.O. called this rationale "novel" and said it was not in keeping with earlier agency decisions in which the behavior of older adolescents was routinely used to predict that of younger ones. The report also noted that the December 2003 advisory committee had voted 27 to 1 that Barr's study had demonstrated that consumers, adolescents included, could use the drug appropriately.

In his rejection letter to Barr, Dr. Galson suggested two ways it could receive approval. First, it could perform another study that included more young adolescents. Or it could seek to sell the drug "behind-the-counter," making it easily available only to women 16 and older, with younger women still needing a prescription.

Barr took the second approach in an application filed in July 2004. Although the agency's rules required it to issue a decision in January, it has delayed doing so indefinitely.

It is unusual for the agency to suggest a means of approval to an applicant only to decide later that its own suggestion might not be appropriate.