The Air Force said Monday that it had fined the former commander of the Dover Air Force Base mortuary $7,000 and suspended his top deputy for 20 days without pay for retaliating against whistleblowers, but it allowed both men to keep their jobs.

The punishment came in response to an independent federal investigation that concluded the mortuary’s leadership had wrongfully tried to fire two subordinates after they reported missing body parts, lax management and other problems at the base that handles America’s war dead.

The former commander, Col. Robert Edmondson, was assessed the fine and given a letter of reprimand for committing reprisals, according to an Air Force statement. Edmondson was also reprimanded in November after the Air Force found that he was responsible for “gross mismanagement” at the mortuary.

His top civilian deputy, Trevor Dean, was suspended for the reprisals. He still works for the Air Force at Dover but voluntarily moved to a non-supervisory job.

The disciplinary measures were imposed after members of Congress and Defense Secretary Leon E. Panetta urged the Air Force to take stronger personnel action late last year at Dover. Some lawmakers pointedly asked why the Air Force had not fired anyone after disclosures that the body of a Marine was mutilated and the partial remains of other service members dumped in a landfill.

Air Force Secretary Michael Donley reviewed the final punishments for Edmondson and Dean and “considers them appropriate,” the Air Force said in its statement. Edmondson and Dean did not respond to e-mails seeking comment.

A third supervisor, Quinton “Randy” Keel, resigned under pressure in February.

The Office of Special Counsel, an independent federal agency that concluded in January that the Dover supervisors had retaliated against whistleblowers, said it was “encouraged” by the moves.

“These actions send a strong signal that employees at all levels will be held accountable for whistleblower reprisal,” said Carolyn Lerner, the head of the agency.

On Friday, the House passed legislation to create a mortuary affairs advisory commission in response to the scandal.

“The command at Dover was so out of touch they seemed surprised that the disclosures about activities there brought disbelief and dismay from the public,” said Rep. Rush D. Holt (D-N.J.), who sponsored the measure. “Clearly, they need an advisory and watchdog committee . . . to help them operate within the bounds of public decency and decorum from now on.”