A year-long Air Force investigation reviewed 14 sets of allegations of improper handling of war remains as reported by three whistleblower workers at Dover Air Force Base, Del. That is where all war dead are received from foreign battlefields to be identified, autopsied and prepared for transfer to their families.
The Air Force inspector general concluded that no laws or regulations had been violated, as alleged, but an independent agency that reviewed the probe said the Air Force failed to accept accountability for its mistakes.
Defense Secretary Leon Panetta has asked for a separate investigation.
The Air Force determined that the mortuary's top leadership failed over time to respond to clear signs of weakness in accounting for human remains - a task the Air Force says it considers one of its most solemn duties.
Two of the three officials who were punished are still work at Dover but not in supervisory jobs. None was fired.
In reviewing the Air Force's probe, the Office of Special Counsel, an independent federal investigative agency, sharply disputed the conclusion that none of the allegations of mishandling of remains amounted to violations of law or regulation. The special counsel submitted its own report Tuesday to the White House and to the House and Senate armed services committees that oversee the Air Force.
The special counsel's office, which triggered the Air Force probe by referring to it the Dover whistleblowers' allegations, said some of the Air Force's conclusions "do not appear reasonable" and in some cases are not supported by available evidence.
"In these instances the report demonstrates a pattern of the Air Force's failure to acknowledge culpability for wrongdoing relating to the treatment of remains of service members and their families," the special counsel's report said.
"While the report reflects a willingness to find paperwork violations and errors, with the exception of the cases of missing portions (of remains), the findings stop short of accepting accountability for failing to handle remains with the requisite `reverence, care and dignity befitting them and the circumstances,"' it said.
In addition to the two cases of lost body pieces, the Air Force reviewed allegations that mortuary officials acted improperly in sawing off an arm bone that protruded from the body of a Marine in a way that prevented his body from being placed in his uniform for viewing before burial. The Marine's family had requested seeing him in his uniform but was not consulted about - or told of - the decision to remove the bone.
The Marine, whose identity was not released by the Air Force, was killed by a roadside bomb in Afghanistan in January 2010. The 2009 cases of lost body pieces also involved troops killed in Afghanistan.
The Air Force inspector general began his investigation in June 2010. It concluded that the mortuary had not violated any rule or regulation by removing the Marine's bone as it did. But the Air Force has since changed procedures to ensure that a representative of the deceased's service - in this case the Marine Corps - has a formal say in whether the family should be contacted before altering the body so significantly.
The Office of Special Counsel took a different view. It noted that the Air Force said the decision not to seek family consent was based on a desire to spare the family "undue distress." But the special counsel said it does not believe the Air Force actually even considered these issues in deciding not to consult the family - "but rather were reasons used to justify their actions after the fact."
A total of four families affected directly by the investigation were told of it last weekend by Air Force officials. In addition to the Marine's family, three military families are affected by the two cases of lost body parts - one related to an Army soldier's remains and two involving remains of Air Force crewmen.
Gen. Norton Schwartz, the Air Force chief of staff, said in an interview with The Associated Press and reporters from three other news organizations that the three senior officials who were disciplined had failed to "connect the dots" that should have framed a set of serious shortcomings at Dover - particularly with regard to keeping track of portions of remains that must be handled and examined.
The three are Col. Robert H. Edmondson, who was in overall command of the Air Force Mortuary Affairs Operations at Dover at the time; Trevor Dean, who was Edmondson's top civilian deputy; and Quinton "Randy" Keel, director of the mortuary division at Dover.
All three declined Tuesday, through the Air Force's office of public affairs, to comment for this story.
Edmondson, who had already rotated out of the Dover job by the time the Air Force probe was over, has been given a letter of reprimand, which makes it unlikely he will get a future promotion. Schwartz said the colonel was deliberately put in a staff, rather than command, job in the Pentagon. Dean and Keel, who are licensed morticians, were dropped a notch in their civilian pay grade and reassigned at Dover.
The three workers who lodged the allegations are still employed at Dover. They are James Parsons, an embalming/autopsy technician; Mary Ellen Spera, a mortuary inspector, and William Zwicharowski, a senior mortuary inspector.
Schwartz, the Air Force chief, said he is confident that investigators got to the bottom of the Dover problem and that corrective actions are now in place.
He discounted any parallel with the Army's discovery of severe mismanagement at Arlington National Cemetery, where investigators found more than 200 mislabeled or unmarked graves in three sections of the cemetery outside the nation's capital.
Schwartz said the Dover matter is different but of great concern.
"We all recognized the gravity of this immediately," he said. "It did not take a rocket scientist to understanding what a profound issue this was," given the Air Force's solemn obligation to properly handle war remains.
To illustrate the burden on the Dover mortuary staff, the Air Force said Dover handled about 4,000 remains and portions of remains between 2008 and 2010. It provided no figures from earlier periods for comparative purposes.
In both 2009 cases of lost body parts the service member's available remains were returned to their families. The mishandled portions - in one case a small piece of soft tissue, and in the other case fragments of ankle bone embedded in human tissue - had been separated from the remains.
The Air Force did not notify the families involved of the failure to account for the missing pieces, and the Office of Special Counsel said it found it troubling that Air Force leaders saw no need for such notification.
One of the two cases of missing parts was in April 2009. It involved fragments of ankle bone embedded in human tissue associated with two crew members recovered from an Air Force F-15 fighter that crashed in Afghanistan. The labeled plastic bag containing this portion of remains was found empty during normal processing, with a slit in the side of the bag. Staff members were unable to account for the missing piece.
Officials said that in no cases do they suspect foul play, criminal acts or deliberate mishandling of the missing pieces.
The other instance was in July 2009 and involved a piece of human tissue an inch or two in length associated with a soldier killed in Afghanistan. As in the April case, the bag containing the piece was found empty, with a slit in its side. The piece of missing tissue was never located.
Another case involved a dispute about the handling of fetal remains shipped to Dover from U.S. military families in Germany. The allegation was that it was disrespectful and a violation of regulations to ship these remains in cardboard boxes rather than in studier containers. The Air Force determined that the use of cardboard boxes - while not "the best option" - did not violate rules. Nonetheless, the practice has been stopped.