The government has almost cleared a backlog of unfinished security clearances for air marshals (search), but other problems remain with the service, congressional investigators said in report Monday.

The General Accounting Office (search), Congress' investigative arm, said that only 3 percent of active air marshals were awaiting their top-secret clearances, down from 25 percent in July. The delay was caused by increased demand for security clearances after the Sept. 11, 2001, terrorist attacks, the GAO said.

The air marshal program mushroomed from a nearly forgotten 32-person unit in 2001 to a sprawling federal law enforcement agency that employs thousands. The exact number is classified.

It has taken time for the agency's management systems to catch up to that growth, the report said.

In its haste to ramp up quickly, the air marshal service hired people after obtaining interim secret security clearances.

Eighty federal air marshals were placed on administrative leave in June because of issues that surfaced during the full background investigations. Two months later, 47 received clearance and returned to work, 19 were denied clearances and seven resigned. Another seven are awaiting top-secret clearances.

The investigators also said the federal air marshal service needs to keep better track of the hours the marshals actually work so it can prevent overscheduling them. If air marshals work too many hours, fatigue could prevent them from concentrating on their mission, the report said.

Air marshals had complained anonymously to the news media and to members of Congress that they were either underworked or overworked.

The report noted that 10 percent of the air marshals hired since the terrorist attacks have resigned, but the agency doesn't collect good information about why they left.

Summaries of the reasons for leaving "are not detailed enough for management to identify and respond to specific problems, such as dissatisfaction with the service's transfer policy," the report said.

The investigators alluded to interviews by the Transportation Department's inspector general that revealed dissatisfaction with the air marshal service's work schedules, aircraft boarding procedures and dress code policy.