The remains from the Pentagon crash site were handled by the military mortuary at Dover Air Force Base, the primary site for caring for America’s war dead.

The Pentagon scrambled Wednesday to try to determine how many victims of the Sept. 11, 2001, attacks had their remains incinerated and dumped in a landfill.

Senior officials acknowledged that they were caught flat-footed by the revelations, made in a Pentagon report released Tuesday, about remains from Sept. 11 being sent to a Virginia landfill, and they pledged further investigation of the matter.

Gen. Norton A. Schwartz, the Air Force chief of staff, said that contrary to the Pentagon report, it did not appear that unidentified remains of victims of the United Airlines Flight 93 crash in Shanksville, Pa., were disposed of in a landfill, “as best we can tell.”

“This is something we need to nail down,” Schwartz said.

He said the practice was limited to the unidentified, partial remains of people who died when American Airlines Flight 77 crashed into the Pentagon, but he could not quantify how many remains were handled in that manner.

Schwartz cited a Pentagon memo from March 2002 directing the military to incinerate “fragmented remains” that had been mixed with “non-biological materials” recovered from the crash site. Other unidentified remains from the Pentagon were cremated and interred at Arlington National Cemetery.

The memo, written by David S.C. Chu, then undersecretary of defense for personnel, did not specify that the incinerated remains be taken to a landfill. Chu did not respond to a phone call and e-mail seeking comment.

The remains from the Pentagon crash site were handled by the mortuary at Dover Air Force Base, the primary site that cares for America’s war dead. Operations at Dover, which the military considers a hallowed site, have come under scrutiny since November, when a series of investigations uncovered reports of missing body parts, a mutilated corpse, fraud and other problems.

Since at least 1996, the Dover mortuary disposed of the unclaimed or unidentified remains of troops first by cremating them and mixing them with medical waste. The mixture was then incinerated and the ashes dumped in a landfill.

Funeral home directors have described the procedure as highly unusual and not in keeping with professional standards for treating the dead with reverence. The practice continued at Dover until 2008, when military officials changed the policy in favor of burying ashes at sea.

Schwartz told reporters Wednesday that there was no excuse for the landfill policy but that the Air Force has worked hard to fix problems at Dover in the past two years.

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

The revelation that at least some remains of Sept. 11 victims were burned and dumped in a landfill was contained in the latter pages of the Pentagon report released Tuesday, which examined operations at the troubled Dover mortuary.

That report, part of a Pentagon-commissioned review led by retired Army Gen. John Abizaid, had few details about the handling of remains from the Sept. 11 attacks. Abizaid declined to elaborate at a news conference Tuesday.

Senior Pentagon officials, including Schwartz, Air Force Secretary Michael Donley and Defense Secretary Leon E. Panetta, all said they had been unaware of what happened.

On Wednesday, the Pentagon said Panetta had ordered staffers to get to the bottom of the matter and to provide answers to relatives of Sept. 11 victims “within the next few weeks.”

“The Department is continuing to assemble records and information on the past practices of disposition of partial remains,” George Little, the Pentagon press secretary, said in a statement. “We intend to make the facts about that past policy known to the loved ones of those who died.”

Stephanie Dunn DeSimone, the widow of Patrick Dunn, a Navy commander who was killed in the Pentagon attack in 2001, said she was stunned to learn that some fragmented remains of the victims may have been disposed of improperly.

“I’m devastated,” she said in an interview. “It’s shocking to hear they were mishandled, especially by the military. The Pentagon has done such a good job for most of us these past 10 years.”

Panetta had previously asked Abizaid to look into reports by The Washington Post that the Dover mortuary dumped the burned partial remains of at least 274 troops in a Virginia landfill between 2003 and 2008.

In an exchange with reporters Tuesday, however, Abizaid said that his primary charge was to make sure that current operations at Dover were fixed, not to reexamine past problems.

On Wednesday, the Pentagon declined to release other documents that might shed light on how human remains from Sept. 11 were handled.

For instance, an appendix to Abizaid’s report cited two 2002 military memos that detailed the incineration of remains from the Pentagon crash site. Officials said the contents were under internal review and could not be released.

Staff writer Matt Connolly contributed to this report.