WASHINGTON — The Air Force mortuary that receives America’s war dead and prepares them for burial lost portions of human remains twice in 2009, prompting the Air Force to discipline three officials for “gross mismanagement,” officials said today.

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 formally identified, autopsied and prepared for transfer to their families.

The Air Force inspector general found no violations of law or regulation in any of the 14 cases, but he cited a series of failures by top officials that seriously undermined the mortuary work of the Air Force, which views the Dover mission as one of its most important duties to military members and their families.

A parallel probe by the Office of Special Counsel, an independent federal investigative agency, took a harsher view of the events at Dover and sharply questioned the Air Force’s “failure to acknowledge culpability for wrongdoing.”

In a report submitted to the White House today, the special counsel 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.

Both investigations focused on several main allegations.

In addition to the two cases in which portions of human remains went missing during processing at Dover, one worker complained about the handling of the remains of a Marine killed by a roadside bomb in Afghanistan in January 2010.

The Air Force reviewed a claim that mortuary officials acted improperly in sawing off an arm bone that protruded from the body of the 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.

In a preliminary communication with the Air Force, the Office of Special Counsel disputed the Air Force’s conclusion that it was not necessary to get specific permission from the Marine’s family in advance.

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.

None of the three Air Force officials found to be at fault at Dover was fired.

The Air Force commander at Dover, Col. Robert H. Edmondson, received a letter of reprimand and was put in a staff job at the Pentagon. Trevor Dean, who was Edmondson’s top civilian deputy at Dover, took a different job at Dover in a lower pay grade. Quinton “Randy” Keel, who was director of the mortuary division at Dover, also was reassigned at Dover in a non-supervisory position.

The three workers who lodged the allegations are still employed at Dover.