Col. Robert Edmondson, left, the former Air Force Mortuary Affairs Operations Center commander, will have harsher penalties imposed on him and another supervisor after a federal probe found they retaliated against subordinates for reporting systematic problems, including cases in which body parts were lost. (Senior Airman Andrew Helmkamp/U.S. Air Force)

The Air Force said Friday it will impose harsher penalties on the former commander and chief deputy of the Dover Air Force Base mortuary after a federal probe found they retaliated against subordinates for reporting systematic problems there, including cases in which body parts were lost.

The Air Force declined to specify what action it will take against Col. Robert Edmondson, the former commander, and his civilian deputy, Trevor Dean, saying only that it had begun disciplinary proceedings that will last into next month. Previously, Edmondson had been issued a letter of reprimand; Dean had been placed in a lesser, non-supervisory position.

The announcement was made in response to an investigation by the Office of Special Counsel, an independent federal agency that protects whistleblowers. The probe found that Edmondson, Dean and another supervisor had provided phony reasons to fire or punish four mortuary workers who had exposed problems there.

Two of the Dover whistleblowers were terminated in 2010 for allegedly watching an X-rated movie at the mortuary, according to the Office of Special Counsel’s report, which was made public Friday. The investigation determined that the film was an R-rated cop flick — “Brooklyn’s Finest,” starring Richard Gere and Ethan Hawke — and that movie-watching was officially encouraged during employee breaks as a way to reduce stress.

The firings came shortly after the two whistleblowers protested an order to saw off the fused arm bone of a dead Marine so he could fit in his dress uniform and casket. One of them, James G. Parsons Sr., an embalming technician, filed complaints about the incident, saying it amounted to mutilation.

“This has probably been the worst two years of my life,” Parsons said in an interview Friday. His firing was overturned after the Office of Special Counsel intervened on his behalf. He said that he was pleased the Air Force had decided to discipline his former bosses, but that he was “anxious to see” their final punishment and whether it sticks.

He blamed Edmondson for most of the problems. “This was his little island, and I don’t think there was much oversight,” Parsons said. “I think that had a lot to do with what happened.”

Edmondson, who is assigned to the Pentagon, did not respond to an e-mail or an interview request placed with Air Force officials. The Office of Special Counsel report concluded that he was the “primary force” behind the effort to retaliate against the whistleblowers.

The Office of Special Counsel said Edmondson wrongly tried to fire another whistleblower, William D. Zwicharowski, in 2010, even though a senior Air Force lawyer warned there was no basis for him to be fired.

The lawyer, whose identity was redacted from the Office of Special Counsel report, said the infractions in question were exceedingly minor and “didn’t pass the smell test.” He also said he was “flabbergasted” when another Air Force official admitted that mortuary supervisors were looking for reasons to “get rid of” Zwicharowski because he had filed whistleblower complaints.

Zwicharowski was placed on leave for several months but ultimately was allowed to return to work. In an interview Friday, he credited the Air Force lawyer and the Office of Special Counsel for saving his job. He said that when he filed a grievance about a suspension he was given in 2009, other Air Force officials at the Pentagon “literally laughed at me. No one was listening.”

The leadership of the Air Force has taken heat for months from lawmakers and veterans groups for not firing Edmondson and Dean despite evidence that they and another supervisor were responsible for “gross mismanagement” at the mortuary that handles America’s war dead. Dean declined to comment for this article.

Another supervisor at the Delaware mortuary, Quinton “Randy” Keel, was demoted but given another job at Dover; he resigned late last month.

Angry lawmakers called the actions a slap on the wrist. Defense Secretary Leon E. Panetta ordered Air Force Secretary Michael B. Donley to reconsider whether stronger punishment was warranted. Upon review, Donley upheld his January decision but reopened the case last month at the request of the Office of Special Counsel.

“The Air Force will not tolerate wrongdoing, especially prohibited personnel practices,” Donley said in a statement Friday. “We are committed to a workplace climate that makes individuals feel confident that they can raise any concerns they may have.”