A U.S. Army carry team moves the transfer case of U.S. Army Spc. Ryan M. Lumley during a dignified transfer at Dover Air Force Base, on December 5, 2011. A mortuary supervisor at the heart of the Dover Air Force Base scandals has resigned. (Mark Wilson/GETTY IMAGES)

A mortuary supervisor at the heart of the Dover Air Force Base scandals has resigned, sparing the Pentagon from a decision on whether to fire him for allegedly lying to investigators, mutilating a corpse and retaliating against whistleblowers.

Quinton “Randy” Keel, 44, formerly the Dover mortuary’s division director, cleaned out his desk at the air base Monday after he tendered his resignation, according to officials familiar with the case. An Air Force spokesman, Lt. Col. John L. Dorrian, confirmed that Keel was no longer employed by the Air Force but declined to comment further.

Keel, of Felton, Del., did not respond to phone messages this week seeking comment.

He was one of three supervisors at Dover whom the Air Force in November accused of “gross mismanagement” at the military’s primary mortuary for handling the nation’s war dead. An 18-month investigation, spurred by whistleblowers who worked for Keel, documented instances of missing body parts and the sloppy handling of human remains, among other problems.

Investigators from an independent agency, the Office of Special Counsel, found that Keel had tried to fire two of the whistleblowers. In November, it accused him of “a pattern of negligence, misconduct and dishonesty.” The office, which handles federal whistleblower complaints, also accused the Air Force of a “failure to acknowledge culpability for wrongdoing relating to the treatment of remains.”

In response, senior Air Force officials stripped Keel of his title. They then transferred him to another management job at Dover created for him, angering the Office of Special Counsel, members of Congress and veterans groups who said he should have been fired.

At the time, senior Air Force leaders defended their actions. Gen. Norton A. Schwartz, the Air Force chief of staff, said the Dover supervisors did not intentionally commit wrongdoing. “This wasn’t a deliberate act, in my personal view,” he said.

Investigators found that Keel ordered an embalmer to saw off the arm bone of Sgt. Daniel Angus, a Marine killed in Iraq, so he could fit in his dress uniform in a casket. Keel overruled objections from mortuary workers that such an act amounted to mutilation and that they lacked permission from the Marine’s family.

Angus’s parents, Kathy and William Angus of Thonotosassa, Fla., remain frustrated with the Air Force’s handling of the scandals at Dover, according to their attorney, Mark J. O’Brien of Tampa.

“They would have preferred that Mr. Keel have been fired months ago, but they are certainly not upset at the news that he resigned,” O’Brien said in an ­e-mail. “However, if nothing else happens in this matter except for one of the major players involved in this cover-up being allowed to resign in lieu of being fired, then the Angus family will not be — nor will they ever be — satisfied.”

James G. Parsons Sr., a mortuary technician who had objected to Keel’s orders to saw off the Marine’s arm, was subsequently fired by Keel after he filed a whistleblower complaint about that and other problems at Dover. Parsons was reinstated to his job after the Office of Special Counsel intervened.

On Friday, Parsons said he was disappointed that Keel was allowed to quit instead of being terminated.

“I understand you can’t take action to prevent someone from resigning, but it would have been nice to see them do something a lot sooner,” he said. “I hate to see anybody lose their job, but if there’s just cause, and I think there was, then it should happen.”

Revelations of missing body parts and the mishandling of corpses stirred widespread anger when they became public in November. Among military personnel, caring for fallen troops with reverence and respect is a sacred obligation, and lawmakers and veterans were horrified to learn what had transpired behind closed doors at the Delaware mortuary.

In December, The Washington Post reported that the Air Force dumped the burned partial remains of at least 274 American troops in a Virginia landfill between 2003 and 2008. The two other supervisors — Col. Robert H. Edmondson, former mortuary commander, and his civilian deputy, Trevor Dean — were disciplined but also did not lose their jobs. Edmondson received a letter of reprimand after he left Dover for a new assignment. Dean voluntarily accepted a lesser position at the mortuary.

On Tuesday, the Defense Department revealed that the Dover mortuary also incinerated and dumped in a landfill some fragmented remains of people who died in the Sept. 11 , 2001, attack on the Pentagon.

After the scandal broke in November, lawmakers and veterans groups criticized Air Force Secretary Michael B. Donley and Schwartz, the Air Force’s top general, for not taking harsher action against the supervisors.

Defense Secretary Leon E. Panetta, after first backing the Air Force leaders, subsequently ordered them to review whether tougher discipline was warranted.

On Tuesday, however, Donley said an “independent assessment” by former officials whom he had commissioned to look into the matter backed up his decision not to fire anyone. He said that review, completed last month, judged that the discipline was “legal, appropriate and well within the bounds of reasonableness.”

On Jan. 30, the Office of Special Counsel completed another investigation, this time concluding that the Air Force had violated the federal Whistleblower Protection Act by retaliating against four Dover employees who had reported problems.

In addition to the firings of Parsons and another employee who was later reinstated, the Dover supervisors suspended two other whistleblowers. One said his bosses tried to justify the retaliation by painting him as mentally unstable.

The Office of Special Counsel urged Donley to impose “substantial” further punishment against Keel and Dean and said it would take legal action if he did not. The agency has the authority to seek discipline against civilian federal employees but not military personnel, such as Edmondson.

On Friday, the Office of Special Counsel issued a statement saying: “It is not surprising that Mr. Keel chose to resign,” given that he was found to have retaliated against whistleblowers. It said that it was still awaiting the Air Force’s “final decisions on disciplinary action for the two supervisors who remain on staff.”

“The government needs to listen to employees who come forward with serious allegations of wrongdoing,” said Carolyn Lerner, the head of the Office of Special Counsel. “And it needs to take disciplinary action when supervisors suppress or punish whistleblowers. Failure to do so sends a chilling message.”

Donley said he is reviewing the matter and will make a decision by the middle of the month.

Schwartz said the Air Force took the whistleblowers’ complaints seriously and moved quickly to investigate problems at Dover once it became aware of them. He said the Air Force would make changes to its managerial and command structure to ensure that future complaints are received more readily.

“It is unfortunate, and it is not something that I’m proud of, that the whistleblowers felt compelled to use other channels to surface their concerns, but I’m grateful that they did, and we’re acting on them,” Schwartz said Wednesday. “That, I think, is what is most important, getting it right today and in the future.