Federal investigators said Tuesday that they had uncovered “gross mismanagement” at the Dover Air Force Base mortuary that cares for America’s war dead after whistleblowers reported horror stories of lost body parts, shoddy inventory controls and lax supervision.

The Air Force admitted that the Dover mortuary misplaced a dead soldier’s ankle and another set of remains that had been stored in a plastic bag. Employees also sawed off the damaged arm bone of a Marine so he could fit in his uniform and coffin — but did not tell his family.

Military officials said the incidents resulted from the strain of handling thousands of dead bodies, some with gruesome injuries that made it difficult to prepare remains for burial.

But the sloppy handling of troops’ remains at Dover painfully undercut the military’s commitment to treat war dead with the utmost honor. “There is nothing more sacred, there is nothing that is a more profound obligation than treating our fallen with reverence, dignity and respect,” said Gen. Norton A. Schwartz, the Air Force chief of staff, who took responsibility for the problems.

The Air Force disciplined but did not fire the mortuary commander and two other senior officials. Some members of Congress called the punishments inadequate, and an independent federal watchdog agency said investigators should have pushed harder to assign blame.

The Air Force and the Army both investigated the complaints about Dover. But the Office of Special Counsel, a watchdog group that receives complaints from whistleblowers and protects them against reprisals, criticized the Air Force’s handling of the situation in unusually sharp language.

In a letter, agency head Carolyn Lerner said the service displayed a pattern of “failure to acknowledge culpability for wrongdoing,” adding that it had managed to “stop just short of accepting accountability.”

Her office said one mortuary official was “untruthful” and tried to obstruct the investigation by firing a whistleblower.

One of the whistleblowers agreed. “The Air Force basically tried to make the Air Force not look too bad,” said James G. Parsons Sr., an autopsy and embalming technician. “They did try to cover it up.”

Schwartz said the Air Force decided not to fire the three mortuary supervisors because “while their performance did not meet standards, this was not a deliberate act.” He also said the Air Force took into account the emotional stress of caring for the remains of thousands of troops killed in battle. “Notwithstanding their faults, this was difficult work.”

The grisly findings at Dover echoed a similar scandal at another hallowed repository for the military’s dead, Arlington National Cemetery. An Army investigation last year documented cases of misidentified remains at Arlington, dug-up urns that had been dumped in a dirt pile and botched contracts worth millions of dollars. The Army Criminal Investigation Command and the FBI are now conducting a criminal probe there.

As news spread of the problems at Dover, Sen. Jon Tester (D-Mont.), a member of the Veterans Affairs Committee, said he didn’t understand why the Air Force continued to employ the three supervisors. “Why weren’t they fired?” Tester wrote Tuesday in a letter to Air Force Secretary Michael B. Donley.

In emotion-laden remarks to reporters, Schwartz said the Air Force became aware of problems at Dover in May 2010 after whistleblowers complained to several agencies. But the Air Force waited more than a year — until last weekend — to notify the families of four deceased service members that their remains had been lost or mishandled.

At first, Schwartz asserted that the Office of Special Counsel had placed “certain constraints” on the Air Force’s ability to notify the families, resulting in the delay. Later, he said the Air Force waited until the investigations were complete so that the families could be fully informed.

The Office of Special Counsel disputed Schwartz’s account. The agency said relatives of fallen service members should have been notified right away, but the Air Force resisted.

Mark Cohen, the deputy special counsel, called Schwartz’s suggestion that the Office of Special Counsel was responsible for the delay “patently false,” adding: “The Air Force has shown as much, if not more, reverence for its image as it has for the families of the fallen.”

In addition to the missing body parts, Parsons and two other whistleblowers alleged that the mortuary kept shoddy records and endangered public health by improperly handling a corpse thought to be infected with tuberculosis.

They also complained that the mortuary permitted an Army hospital in Germany to ship fetal remains in reused cardboard boxes back to the United States for burial instead of in aluminum transfer cases.

The Air Force inspector general confirmed many of the facts in the complaints and documented a pattern of “gross mismanagement.” But the inspector general determined that there was not enough evidence to prove the three supervisors had personally broken any regulations.

As a result, the supervisors received relatively lenient punishments. Col. Robert H. Edmondson, who served as mortuary commander from January 2009 to October 2010, was issued a letter of reprimand — usually a career-ending punishment for an officer. He is still on active duty but has been reassigned.

Quinton R. “Randy” Keel, a civilian who served as division director at the mortuary, was demoted in August. He has been assigned to another job at Dover Air Force Base and no longer works in the mortuary.

The Office of Special Counsel chided the Air Force for not taking stricter action. It noted that investigators concluded Keel had falsified records, tried to fire two employees for cooperating with the probe and gave a version of events that was “wholly inconsistent with the facts.”

The top civilian deputy of the mortuary, Trevor Dean, also still works at Dover. The Air Force said he voluntarily accepted a transfer to a lesser position in September.

Dean, Edmondson and Keel all declined a request for comment through an Air Force spokesman.

Troubles first surfaced in April 2009 when technicians noticed something amiss while conducting an inventory of body parts stored in a walk-in refrigerator.

A sealed plastic bag that was supposed to contain a shattered ankle from a soldier killed in Afghanistan was empty, according to the investigations. The ankle had been stored in the refrigerator seven months earlier, but the plastic bag was slit at the bottom and a frantic search turned up no sign of the remains.

About the same time, supervisors learned that a similar problem had occurred three months earlier, when two plastic bags containing body parts were also found slit and emptied. In that incident, technicians found what they believed were the missing remains in trays on storage racks underneath the bags.

Another empty plastic bag was found in July 2009. Missing was a four-inch-long piece of flesh recovered from an F-15 fighter jet crash in Afghanistan; two airmen had died and medical examiners weren’t certain to whom the missing body part belonged. It was never located.

Another problem surfaced in January 2010 when a Marine killed by a roadside bomb in Afghanistan arrived at the mortuary. Although his body was shattered from the waist down, his family requested that he be buried in his dress uniform.

Morticians tried to honor the request but couldn’t fit the Marine into his uniform or a coffin because a section of his left arm was sticking out after trauma suffered in an explosion in Afghanistan. The report from the Office of Special Counsel said the arm was fixed at a 90-degree angle and could not be moved into alignment during embalming.

Keel ordered a mortician to saw off the bone and place it in a bag in the casket. Some technicians at Dover objected, saying that it amounted to “mutilation” and that the family should have been consulted.

The Air Force inspector general concluded that Keel did the right thing because he was attempting to honor the family’s wishes.

Investigators from the Office of Special Counsel, however, disagreed, saying the case was inconsistent with “the highest standards in the funeral service profession.”

Staff writers Michael E. Ruane and Christian Davenport and staff researcher Julie Tate contributed to this report.