WASHINGTON, Sept. 23 - Lester M. Crawford, the commissioner of food and drugs, resigned abruptly on Friday, causing further upheaval at an agency that has been in turmoil for over a year.

Dr. Crawford, who was confirmed just two months ago, on July 18, after serving as acting commissioner for over a year, did not say why he was stepping down.

Senior officials at the Food and Drug Administration said they were stunned to learn of the resignation in an e-mail message from Dr. Crawford, who also sent a letter to President Bush stating that he was resigning "effective immediately."

Michael O. Leavitt, the secretary of health and human services, accepted the resignation and thanked Dr. Crawford for his service. Christina Pearson, a spokeswoman for Mr. Leavitt, refused to say whether Bush administration officials had asked for the resignation.

"I can't comment," Ms. Pearson said. "This is a personnel issue."

In recent weeks, consumer advocates and scientists inside and outside the agency had complained that scientific decisions were being warped by politics.

On Thursday, a commentary in The New England Journal of Medicine titled "A Sad Day for Science at the F.D.A." said that "recent actions of the F.D.A. leadership have made a mockery of the process of evaluating scientific evidence," disillusioned many scientists, "squandered the public trust and tarnished the agency's image."

Mr. Bush said he intended to name Dr. Andrew C. von Eschenbach, director of the National Cancer Institute, to be acting commissioner of food and drugs.

Dr. Crawford, a veterinarian and expert on food safety, was named deputy commissioner of the agency in early 2002 before his tenure as acting commissioner. In that time the agency has been rocked by disputes over many issues, including the safety of painkillers like Vioxx, the regulation of heart defibrillators and other devices, and delays in deciding whether to allow over-the-counter sales of an emergency contraceptive.

Critics, including members of Congress from both parties, say the agency has not provided the public with enough information about the risks of drugs and devices.

"In recent years the F.D.A. has demonstrated a too-cozy relationship with the pharmaceutical industry and an attitude of shielding rather than disclosing information," said Senator Charles E. Grassley, Republican of Iowa and chairman of the Senate Finance Committee.

Senator Barbara A. Mikulski, Democrat of Maryland, said the agency had been "politicized and degraded" under Dr. Crawford, whose leadership she described as "tepid and passive."

At the F.D.A., as at the Federal Emergency Management Agency, Ms. Mikulski said, the Bush administration has brought "incompetent leaders into critical positions."

Before the Senate confirmed Dr. Crawford, a Senate committee looked into accusations that he was having an affair with a woman who worked in his office and that he had wasted government money by taking her on official trips when she was not needed. An anonymous letter also suggested that Dr. Crawford had helped the woman secure a promotion to a higher-paying job.

An inquiry by the inspector general of the Department of Health and Human Services found some contradictions in statements by Dr. Crawford and the woman. Investigators found a close personal relationship between them but no evidence of an extramarital affair.

The committee chairman, Senator Michael B. Enzi, Republican of Wyoming, said at the time that the inspector general had found no merit to the charges leveled at Dr. Crawford. No senator wanted to pursue the issue further.

Commentary:
Everything the Bush White House and the GOP touches stops working. Intelligence agencies don't work, FEMA doesn't work, deficits have been soaring for five years and we still have three more years of this inanity. Can we survive three more years of conservatism?