The Justice Department's second-in-command, James B. Comey, is clearing out his desk today to take a job as Lockheed Martin Corp.'s general counsel. The department's sprawling criminal division has been without a permanent chief for three months. And two other divisions covering antitrust and civil rights investigations are operating under temporary leadership.

Amid a major department reorganization, a Senate battle over the Supreme Court and an ongoing probe into the leak of a CIA operative's name, the Justice Department is stuck with vacancies in some of its most high-profile and politically sensitive jobs.

Justice officials say they are particularly concerned about the appointments for deputy attorney general and criminal division chief, which have been held up by disputes in the Senate and are unlikely to be approved until mid-September at the earliest.

The delays have resulted in a rare bout of friction between Congress and Attorney General Alberto R. Gonzales, who has vowed to mend frayed relations between Justice and Capitol Hill since his contentious confirmation battle early this year.

"There's a huge concern that we're sitting without confirmed leadership for this many weeks," said one senior Justice official, who spoke on the condition of anonymity because of ongoing negotiations over the appointments.

The candidate to replace Comey, former deputy White House counsel Timothy E. Flanigan, came under sharp questioning from some senators last month about his role in setting U.S. policy on torture and his ties to lobbyist Jack Abramoff, who was indicted yesterday. A confirmation vote has yet to be scheduled.

The Judiciary Committee's chairman, Sen. Arlen Specter (R-Pa.), indicated during a July 26 confirmation hearing that he was dissatisfied with some of Flanigan's responses and hinted that he might not support his appointment.

Perhaps the most intractable disagreement centers on Alice Fisher, a Justice official under Attorney General John D. Ashcroft. She is nominated to head the criminal division. A vote on Fisher's appointment has been blocked by Sen. Carl M. Levin (D-Mich.), who is seeking information from the administration related to detainee-abuse allegations. Levin has placed a hold on Fisher's nomination, taking advantage of long-standing rules allowing one senator to block a nominee, according to Senate aides and Justice officials.

The standoff stems from an FBI e-mail revealed during recent litigation over detainee-abuse allegations in which the author writes: "In my weekly meetings with DOJ we often discussed [Defense Department] techniques and how they were not effective or producing intel that was reliable," adding in a second sentence that Fisher and other Justice officials "all attended meetings with FBI."

To Levin and other Democrats, including Sens. Richard J. Durbin (Ill.) and Edward M. Kennedy (Mass.), the e-mails indicated that Fisher may have participated in discussions of FBI objections to the tactics used by Defense Department interrogators at Guantanamo Bay, Cuba, and other detention facilities.

Fisher said in written responses to the Judiciary Committee that she did not recall participating in discussions of specific interrogation techniques. According to a follow-up letter from Assistant Attorney General William E. Moschella, the unidentified author of the FBI e-mail said that Fisher had not participated in such discussions and that he did not mean to imply that she had.

But Levin and other Democrats want to interview the FBI agent themselves, a request that the Justice Department has refused.

The Justice vacancies come at a busy time for the department. Under a reorganization ordered by President Bush, Justice officials are working on plans to create a national security division within the department to oversee counterintelligence and counterterrorism investigations -- much of which is now handled by the criminal division that Fisher has been nominated to lead.

Comey, the departing deputy attorney general, has also had the task of overseeing special counsel Patrick J. Fitzgerald's probe into the leak of CIA operative Valerie Plame's identity.

Justice officials expect to announce today that Comey will be replaced temporarily by Associate Attorney General Robert D. McCallum. Officials have declined to say whether McCallum -- a Yale classmate of the president's as well as a longtime friend -- would be tapped to oversee the Plame investigation.

The departure of second-in-command James B. Comey creates another key vacancy at a Justice Department facing critical issues.