Beck didn’t return a telephone call from the AP seeking comment. The FAA report said the controller who made the error initially thought he’d been told the planes were at the same altitude, which is why he told the Air Force jet to go up to 3,000 feet.

The controller has been removed from directing air traffic and is “currently assigned to administrative duties while the FAA evaluates the individual’s future status with the agency,’’ the FAA said in a statement.

FAA officials are “committed to ensuring the safety of our nation’s airspace for the traveling public, and we take seriously and investigate all reported infractions,’’ the statement said. “We are working with (the National Air Traffic Controllers Association) to implement a professional standards pilot program that will help improve performance levels and conduct among employees.’’

The program, which is in place at 21 facilities so far, provides an opportunity for employees to address the performance or conduct of their peers, the FAA said. The agency employs about 15,600 controllers and has fired more than 130 since October 2009.

Ralph Humphrey, Beck’s former boss, said he tried repeatedly last year to get the controller fired, but FAA officials in Washington ignored his requests.

“It’s typical of trying to get rid of problem employees’’ at FAA, said Humphrey, who was the air traffic manager in Gulfport until he retired in January. “It is damn difficult to get rid of an employee for cause.’’

One reason is that union officials exploit complex employee protection rules even when controllers are unfit, Humphrey said.

Efforts to obtain comment from the controllers association were not immediately successful.