WASHINGTON (Reuters) - Unidentified remains from the September 11, 2001, crash site in Shanksville, Pennsylvania, do not appear to have been handled by the military's main mortuary, as suggested in an independent report, the top U.S. Air Force general said on Wednesday.

U.S. Air Force Chief of Staff General Norton Schwartz said Air Force officials were still trying to confirm much of the information in the report, which said partial remains from some people killed in the attack ended up in a landfill.

He said the mortuary at Dover Air Force Base followed Pentagon orders for incinerating and disposing of an unknown number of partial remains that were unidentified and co-mingled with material from the Pentagon crash site, not other September 11 sites.

Schwartz cited a previously undisclosed March 2002 memo from then then-undersectary of defense for personnel and readiness that laid out instructions for dealing with remains from the attack on the Pentagon, not those from the Pennsylvania crash site or the attack on the World Trade Center in New York.

David Chu was the undersecretary of defense for personal and readiness at that time.

"It applies to the fallen from the Pentagon," Schwartz told reporters at a breakfast meeting. "As best as we can tell, this does not apply to those fallen in New York, or those from Shanksville."

Retired General John Abizaid said on Tuesday that an independent review commissioned by the Pentagon found that unidentified remains from the Pentagon and Shanksville sites ended up in a landfill.

A group representing victims of the crashed United Airlines flight in Pennsylvania has questioned the report's assertion about remains being shipped to the air base in Dover, Delaware.

Lisa Linden, a spokeswoman for Families of Flight 93, which crashed in Shanksville, said the remains from the crash were under the control of the Somerset County coroner.

Pentagon Press Secretary George Little said the Defense Department was continuing to assemble records and information on the past practices of disposition of partial remains, and would brief September 11 families in the next few weeks on its findings.

"We fully understand and want to address the questions families might have about the previous disposition policy that ended in 2008," Little said. "We intend to make the facts about that past policy known to the loved ones of those who died."

CATEGORIES OF REMAINS

Schwartz said Dover had followed guidance issued in the March 2002 Pentagon memo for how to dispose of three categories of unidentified remains.

Unidentified remains from the Pentagon were to be cremated and sent to Arlington National Cemetery, while terrorist remains were to be sent to the FBI.

A third category of remains, which were unidentified and mixed with material from the Pentagon crash site, were to be cremated and disposed of essentially as medical waste, a practice that he said was "accepted practice" at the time, but has since been discontinued.

The report raised further questions about the reputation of the Dover mortuary after last year's revelations that it mishandled the remains of dead from wars in Iraq and Afghanistan. This included losing body parts twice and allowing the partial remains of at least 274 troops to be dumped in a Virginia landfill. That policy was abandoned in 2008 and all partial remains are now buried at sea.

Dover, which is under the control of the Air Force, is the main entry port for returning war dead from the conflicts in Iraq and Afghanistan.

Schwartz said Dover personnel followed the Pentagon's instructions at the time. He said he was not trying to justify the process, and the Air Force had changed its process in 2008.

"We have endeavored since 2008 to ensure that we treat the fallen with the dignity and respect and, in fact, the reverence that they and their families deserve," he said.

"This a no-fail business," he added. "This is one of those areas where perfection is the only standard, and any deviation from that is not only a disappointment, it's an affront to the families of the fallen and our expectations of ourselves."

(Reporting By Andrea Shalal-Esa; Editing by Philip Barbara)