Investigators have found "gross mismanagement" at the US Air Force mortuary that receives the country's war dead, with body parts lost in two cases and remains of others mishandled, officials said Tuesday.

After allegations from whistleblowers at the Dover Air Force base mortuary, an Air Force investigation found two "portions of the remains" of fallen troops were lost and other problems at the morgue, said General Norton Schwartz, the Air Force chief of staff.

New procedures have been put in place at the mortuary and the commander at the morgue -- a colonel -- and two civilian officials were disciplined over the episode but were not sacked, Schwartz told reporters.

While the three supervisors had failed to meet the high standard required, the mistakes were not "a deliberate act," he said.

The mistakes at Dover echoed a scandal that erupted last year at Arlington National Cemetery, the country's hallowed ground for war dead, with investigators finding cases of misidentified remains and mismanagement.

Following an Army probe, the bungling at Arlington is now the subject of a criminal investigation.

Schwartz said he and the civilian head of the Air Force, Michael Donley, took personal responsibility for the missteps at the Dover mortuary.

"There is nothing more sacred... than treating our fallen with reverence, dignity and respect," said Schwartz, looking solemn and his voice cracking with emotion. "This is tough stuff."

But the Air Force's conclusions were at odds with a separate probe by the Office of the Special Counsel, an independent government investigative agency, which rebuked Air Force leaders over their response to whistleblower complaints.

The Air Force has made important changes in its procedures but "it has not taken sufficient disciplinary action against the officials responsible for wrongdoing," the special counsel's office said in statement.

The then military commander of the morgue received a letter of reprimand and was shifted to a job without management duties while the two civilians received a cut in pay and reassigned to other positions, the Air Force said.

The special counsel's office also said it is investigating allegations from the three whistleblowers at Dover "that the Air Force retaliated against them in myriad ways, including an attempt to terminate the employment of one of them."

At Tuesday's press conference, the Air Force acknowledged that one of the whistleblowers was fired but was later reinstated.

Three employees at the mortuary alarmed at the sloppy handling of remains first alerted authorities in complaints filed last year.

The subsequent Air Force investigation found that one dead Army soldier's ankle was lost and that flesh belonging to one of two airmen killed in a F-15 crash was also lost, according to media reports citing investigators.

In another case, mortuary workers were preparing the body of a dead Marine killed by a roadside bomb for a funeral and sawed off a protruding arm bone so that he could be put in a dress uniform.

But the mortuary staff failed to consult his family beforehand, Schwartz said.

Families of the dead troops affected by the mistakes were not informed of the problems until the past week because the Air Force was constrained by the special counsel's office, the general said.

But the head of the office, Carolyn Lerner, told National Public Radio that the general's portrayal was "patently false" and that her agency had urged the Air Force to notify the families dating back to March.

Defense Secretary Leon Panetta, however, backed the Air Force's actions in a statement issued Tuesday and endorsed plans to set up an independent panel, led by former surgeon general Richard Carmona, to review operations at the Dover mortuary.

All American service members killed in combat abroad are transported to the Dover base, where they are identified and prepared for transfer to their families. Since 2003, the mortuary has received the remains of more than 6,300 dead troops, mostly from the wars Iraq and Afghanistan.