The agency's director, Thomas Quinn, announced earlier this week that he will retire on Feb. 3.
"I am proud of the men and women of the FAMS and salute you for your dedication and performance in fulfilling our mission," Quinn said in a memo to employees. "I leave knowing that the Federal Air Marshal Service is an effective, competent federal law enforcement organization that will continue to be an important contributor to the security of the homeland."
Quinn, a former Secret Service agent, took over FAMS after the Sept. 11, 2001, terrorist attacks. He oversaw a dramatic expansion of the service, which puts armed undercover agents on airplanes.
FAMS, which is part of the Transportation Security Administration, received widespread public attention in December when air marshals shot and killed a mentally unstable and unarmed passenger in Miami. The shooting is under investigation.
Quinn had a rocky relationship with some rank-and-file air marshals and other members of the federal law enforcement community, especially over the agency's dress code and the ability of marshals to speak freely about problems without punishment. The Federal Law Enforcement Officers Association, for example, had called for his resignation.
"The smartest thing they can do is put somebody in who can start a clean slate," said an air marshal who asked to remain anonymous.
Some federal law enforcement officers said morale at the agency has dropped to dangerously low levels. Government Executive first reported last month that air marshals are thinking about leaving the service to work for the Border Patrol, which is on a hiring spree.
"It's unfortunate that the adversarial relationship existed but we certainly think things will improve," said a well-placed source, who requested anonymity. "We don't want to use his departure as a means to scrape open the wounds."
"The issues remain irrespective of who the director is," the source added.
Different reasons surfaced Friday for why Quinn finally decided to retire.
The source said the relationship between Quinn and TSA Administrator Edmund "Kip" Hawley apparently had started to sour, especially concerning whether air marshals would be given criminal investigative training and experience and placed on a career path to become criminal investigators.
"I don't think he's going on the happiest of terms," the source said. "I think ultimately he wasn't as successful as he thought he'd be in getting his way with Hawley. The way things are shaping up in TSA is not Tom Quinn's vision. It's Hawley's vision."
Quinn, for example, supports giving air marshals criminal investigative training. But it is unclear where Hawley stands. TSA referred questions concerning Hawley's position on the subject to FAMS.
FAMS spokesman Dave Adams was unable to find out Hawley's position by press time.
The Government Accountability Office reported in November that DHS has made limited progress in enhancing career opportunities for air marshals. A March 2004 study concluded that FAMS could experience a decline in employee morale and an increase in attrition if it fails to improve career development and promotion opportunities.
"I sincerely hope that Mr. Quinn's departure is a personal decision and not a further indication of transition problems at TSA," said Rep. Bennie Thompson, D-Miss., ranking member of the House Homeland Security Committee. "I understand that the decision to alter the air marshals' duties has met with some resistance."
The air marshal noted that several investigations into FAMS management have been conducted during the past few years. "I think that these investigations are finally growing legs," the marshal said.
Adams denied that Quinn is leaving for any reason other than that he wants to retire. Quinn feels the service has reached a maturity level and has enough competent managers for him to step down, Adams said.
"You're reading too much into why the director left," Adams said. "This was a personal decision. The director had been thinking about it for a long time, and he finally decided it was time for him to retire."
He said the relationship between Hawley and Quinn has been "outstanding," adding that the two have known each other since early 2002.
"I commend Tom for his remarkable service and lasting contributions to our nation's security," Hawley said in a statement. "I will miss his wise counsel, class and good humor. He made a lasting mark as a man of integrity and honor, who answered the call when his country needed him."