The Senate confirmed acting Commissioner Lester M. Crawford as the permanent head of the Food and Drug Administration yesterday, five contentious months after he was nominated by President Bush.

Crawford won a comfortable 78 to 16 majority, but before the vote, he was subjected to sharp criticism from a bipartisan bloc of senators that included four Republicans. Although some praised his long experience at the FDA, others said he was part of a system that needs to be shaken up.

The FDA, which regulates one quarter of the nation's economy, has been without a permanent commissioner for more than half of Bush's presidency, and most recently since spring 2004. The agency's need for stable leadership was cited by some senators as a reason to confirm Crawford.

"While I respected the right of my colleagues to disagree with a president's choice, in the end, I believe we have made the right decision to promote Dr. Crawford," Sen. Mike Enzi (R-Wyo.), who shepherded the nomination through the Senate health committee, said in a statement. "He has a long and distinguished history of leadership and public service, and I look forward to his continued work in promoting and protecting the public health."

But Sen. Charles E. Grassley (R-Iowa), who has been an increasingly vocal critic of the agency, spoke strongly against the nomination.

"It is becoming more and more obvious to me that FDA is plagued by structural, personnel, cultural and scientific problems," said Grassley, who as chairman of the Senate Finance Committee has held hearings into the FDA's handling of drug safety issues.

"Those problems should be equally obvious to Dr. Crawford," Grassley said on the Senate floor. "But under the leadership of Dr. Crawford, the FDA appears to be in a state of denial. Over the past 18 months, Dr. Crawford has not stepped up to the plate. I have seen no recognition of the depth and breadth of the problems at the FDA. I have only seen a few short-term Band-Aids."

Crawford's leadership of the agency was also criticized by senators unhappy with its handling of an application to make the "morning-after pill" Plan B a nonprescription drug. Sens. Patty Murray (D-Wash.) and Hillary Rodham Clinton (D-N.Y.) had placed holds on his nomination, saying that the agency was refusing to make a decision on the controversial proposal, which is opposed by some social conservatives but was overwhelmingly supported by the agency science staff and an expert advisory panel. The two senators lifted their hold Friday after receiving assurances that the FDA would make a decision by Sept. 1.

"While I was pleased to receive assurances that the agency will, in the coming weeks, deliver a long overdue decision on Plan B, concerns about Dr. Crawford's leadership remain," Murray said in a statement. "I have been continually concerned during Dr. Crawford's tenure that FDA hasn't shown the independence and adherence to science necessary to inspire public confidence."

Crawford won important support from Sen. Edward M. Kennedy (Mass.), the ranking Democrat on the health committee.

Kennedy told his colleagues that "under Dr. Crawford's leadership at FDA, we have seen stepped up efforts to monitor drug safety and to inform patients and doctors about the risks of drugs. We have recently seen increased scrutiny of drug advertising. . . . Clearly more must be done, and with a commissioner in place, we can work more effectively on the key issues facing the agency, from how FDA monitors drug safety, to ways to address flu vaccine shortages, to how it handles conflicts of interest on its advisory committees, and how it has acted on Plan B."

Soon after Crawford was nominated, Enzi received anonymous allegations that the acting commissioner had an improper relationship with one of his senior staff members and had given her undeserved promotions. The allegations were investigated by the inspector general's office, which reported that there was no evidence of an affair but that there were conflicting accounts of how and why the woman was promoted.

Crawford, 67, has held numerous senior positions at the FDA and the Agriculture Department and has especially deep experience with food safety and animal health.

Lester M. Crawford, the acting FDA commissioner nominated by President Bush to assume the post permanently, was criticized by some senators.

Sen. Charles E. Grassley (R-Iowa) spoke out against the nomination. Sen. Edward M. Kennedy (D-Mass.) backed Crawford's leadership at FDA.