An inspector general's investigation into acting Food and Drug Administration Commissioner Lester M. Crawford's relationship with an employee who won a controversial promotion under his leadership found contradictions between Crawford's version of events and those of the woman and another top agency official.

The investigation did not corroborate other allegations, including one that Crawford and the woman were having an extramarital affair. Based on the findings, Sen. Mike Enzi (R-Wyo.) said yesterday that he would move to have his committee endorse Crawford's nomination to be permanent commissioner of the agency.

The investigation, which has held up Crawford's nomination for two months, was sparked by an anonymous letter alleging that the acting commissioner had improperly promoted to the federal Senior Executive Service (SES) a woman with whom he was having a possibly intimate relationship.

In a letter to Enzi, chairman of the Senate Committee on Health, Education, Labor and Pensions, the inspector general reported "inconsistencies" between the accounts given by Crawford and the woman regarding whether he provided her with inappropriate help in preparing the complicated SES application. The woman said Crawford assisted her, but Crawford denied doing so, saying twice that he provided her only with "moral encouragement." Enzi did not disclose the woman's name or position.

In addition, the report said Crawford -- who formally nominated the woman for the prestigious career executive service rank -- told investigators that he did so on the recommendation of another administrator in his office. But "this administrator stated that he made no such recommendation and that he had previously expressed concerns about [the woman's] qualifications to join the SES," the inspector general reported.

The SES consists of about 6,000 highly compensated career employees, out of 1.8 million federal civil servants, who are chosen for their executive and leadership qualities. Before the inspector general's investigation, numerous FDA officials had privately questioned the woman's fast rise to the highest level of FDA leadership and her lack of a doctoral degree. There are 44 SES employees with lifetime positions in the 10,000-employee FDA.

Michael E. Little, deputy inspector general for the Department of Health and Human Services, said in his letter to Enzi that Crawford and the woman signed statements denying an affair, but investigators did find a close personal or "father-daughter" relationship between them. The investigators examined more than 5,700 e-mail messages between the two.

The FDA declined to comment.

In a statement accompanying the report, Enzi said, "I am pleased that the IG has completed his work and found no merit to any of the charges leveled at Dr. Crawford." Enzi said he continues to have "full confidence" in Crawford.

Some disagreed with Enzi that the accusations against Crawford have been resolved.

"The IG's report does not put to rest the larger question about Crawford's questionable track record as a manager," said Kirsten Moore, director of the Reproductive Health Technologies Project, a women's health advocacy organization. "The FDA -- and indeed the public -- deserves a commissioner with the integrity to put the public interest ahead of his personal agenda. The IG's report fails to reassure us that Crawford meets that standard."

The acting commissioner faces continuing obstacles to being confirmed. Sens. Hillary Rodham Clinton (D-N.Y.), Patty Murray (D-Wash.) and Tom Coburn (R-Okla.) have said they will place holds on the nomination because of unresolved FDA actions on issues involving reproductive health. Clinton and Murray said they will hold up the nomination over the agency's failure to act on an application to make the emergency contraceptive Plan B available without a prescription, and Coburn has said he will do so over the FDA's failure to re-label condom packages, as required by a 2000 law.

Further reflecting the possible difficulties ahead, Laura Capps, a spokeswoman for Sen. Edward M. Kennedy (Mass.), the ranking Democrat on the committee, said the senator believes "we can now move on to the substantive issues of the nomination, such as Plan B."

The FDA has been without a permanent commissioner since March 2004 and has had acting leadership for more than half the time President Bush has been in office. In his statement, Enzi said the FDA needs a permanent leader because an acting commissioner "simply lacks the mandate for action that comes through the constitutional process of nomination by the president and subsequent confirmation by the Senate."

The allegations also raised questions about the amount of travel Crawford and the woman did together at taxpayers' expense. The inspector general's report did not address that issue, but it did examine charges that the woman used her government-issued credit card once for a personal item while traveling and that she did not pay her credit card bill on time. The report said that those problems were handled appropriately and that Crawford "provided her with guidance on the proper use of the card."

Crawford has served as deputy and acting director of the FDA and as administrator of the Agriculture Department's Food Safety and Inspection Service. Trained initially as a veterinarian, he also earned a doctorate in pharmacology from the University of Georgia.

Lester M. Crawford was nominated for the job he is temporarily doing.