The former interim director of Dover Air Force base says superiors in military directed that the ashes be mixed with medical waste and handed over to a contractor for disposal. (Steve Ruark/AP)

Officials at an Air Force mortuary pushed to have some cremated remains from victims of the Sept. 11 attacks buried at sea, but they were overruled by higher-ups in the military who insisted on a plan that resulted in the ashes being dumped in a landfill, according to a mortuary official.

William D. Zwicharowski, a civilian who served as interim director of the mortuary at Dover Air Force Base in 2002, said in an interview that he was still pained by the outcome and wished he had resisted the order more strenuously.

“We fought the fight, but I had zero clout back then,” he said. “The decision was made at a higher level. Had I had the experience I have now, 10 years later, I would have stood up and probably just not done it.”

A Defense Department review of operations at the Dover mortuary revealed last week that some unidentified human remains recovered from the crash of American Airlines Flight 77 at the Pentagon were incinerated and dumped in a landfill.

The disclosure stunned senior military leaders, lawmakers and victims’ families, who had assumed that all unidentified remains from the attack had been cremated and buried together as a group at Arlington National Cemetery.

Since then, Pentagon officials have scrambled to piece together what happened, and why.

Zwicharowski, who still works at Dover, is one of four whistleblowers there who have reported other problems at the mortuary to investigators, including accounts of missing body parts and lax management. He is the first one directly involved in the handling of the Sept. 11 victims’ remains to speak out publicly about what transpired.

Recalling the events after Sept. 11, 2001, he said that both he and the Air Force commander at Dover felt strongly that it was more appropriate and dignified to bury a special collection of unidentified ashes at sea, but that their suggestion was repeatedly denied by superiors in the Air Force, the Army and the Pentagon, who wanted the remains treated differently because they were ingrained with “non-biological materials” from the crash site, such as concrete and other debris.

The superiors — whom Zwicharowski declined to identify — directed that the ashes be mixed with medical waste instead and handed over to a contractor for disposal, he said. Military officials have since acknowledged that the contractor incinerated the mixture and dumped the residue in a landfill. Neither the contractor nor the landfill has been publicly identified.

To buttress his account, Zwicharowski shared several e-mails from July and August 2002 in which military officials discussed what to do with the ashes. He redacted the names of officials from the e-mails, saying he didn’t want to blame individuals.

Pentagon officials acknowledged that they have copies of the e-mails. An Air Force spokesman, Lt. Col. John L. Dorrian, declined to comment but did not dispute Zwicharowski’s account.

Defense Secretary Leon E. Panetta has directed Pentagon officials to get to the bottom of the matter and brief relatives of people killed in the crash of American Airlines Flight 77 later this month. George Little, a Pentagon spokesman, declined to comment on Zwicharowski’s assertions but said the Defense Department is “assembling the facts on past policies and practices” at Dover.

Most unidentified human remains from the Pentagon were cremated and interred at Arlington National Cemetery.

It remains unclear how many remains were ultimately incinerated and disposed of in the landfill.

But Zwicharowski said those remains filled the bottom of a single transfer case — a casket-shaped container used by the Dover mortuary — about two or three inches deep.

He said he personally witnessed the cremation of the remains at a funeral home in Dover on July 26, 2002.

Afterward, he said, he repeatedly pressed his superiors to allow him and the funeral home to dispose of the ashes by burying them at sea.

He said his immediate boss at Dover, the commander of the Air Force’s 436th Air Wing, agreed. But the commander stipulated that they first needed to win approval from Army officials — who were in charge of the military’s overall mortuary policy and responsible for regulations at Dover.

“I’m still sensitive to the fact that there are elements of many loved ones involved, even though we don’t know who,” the Air Force commander wrote in an e-mail to Zwicharowski on July 26, 2002, adding that he thought it would be dignified to inter the ashes “in a ‘quiet placement’ somewhere.”

The next day, July 27, the Air Force commander followed up with another e-mail, endorsing Zwicharowski’s burial-at-sea suggestion but reminding him that it was necessary to get the Army’s approval.

“May be better to scatter the ashes at sea in that it represents neutral territory,” the commander wrote. “Have them hold the ashes until you can get the Army (executive agent) to state in writing just how they would like the ashes disposed of.”

Zwicharowski declined to identify the Air Force commander. Military records show that the 436th Air Wing commander at the time was Col. Scott E. Wuesthoff. Now retired, Wuesthoff did not return a phone call seeking comment.

On Aug. 7, 2002, an unidentified official at the Air Mobility Command at Scott Air Force Base, Ill., sent Zwicharowski an e-mail directing that the ashes be disposed of with medical waste, and incinerated. The official said leaders at the Army’s Personnel Command were in “complete agreement.”

“We shouldn’t attempt to spread the residue at sea, as it could possible send a message to the next of kins that we are disposing human remains, and that is not the case,” the Air Mobility Command official wrote.

Zwicharowski said it was clear to everyone involved that the remains in question did in fact contain cremated human body parts, however small or fragmented. Despite efforts to persuade his superiors to reconsider, he said their order to incinerate the remains was carried out in August 2002.