Partial remains of some victims of the September 11 attacks were dumped in a landfill, the Pentagon revealed on Tuesday for the first time, issuing a report that exposed years of bungling at the US military's most important mortuary.

The portions of remains that ended up at a landfill came from the 2001 attacks on the Pentagon and from a hijacked airliner that went down in Shanksville, Pennsylvania, on 9/11, according to the report by an independent panel.

The revelation came from a review of the troubled mortuary at Dover Air Force Base, which has been blamed for mishandling the remains of some troops killed in the wars in Iraq and Afghanistan.

The details about the 9/11 remains were mentioned only in passing in the report, which focused on how to fix management problems at the troubled mortuary.

Any remains related to 9/11 carry a special significance for Americans and the White House promptly issued a statement, saying the Pentagon was taking steps to ensure such mistakes ‘never happen again.’

"We are deeply concerned about reports that in 2001, some unidentified portions of remains from the 9/11 attacks were disposed of in a landfill, and about the unacceptable handling of remains at Dover," the White House said.

Officials said it was unclear how many victims might be involved or whether some of the remains belonged to the Al-Qaeda hijackers.

The military had acknowledged last year that some portions of remains of fallen soldiers at the Dover mortuary in Delaware had been incinerated and sent to a Virginia landfill, a practice that was halted in 2008.

The military now disposes of unidentified cremated remains at sea.

But the review released on Tuesday said "several portions of remains from the Pentagon attack and the Shanksville, Pennsylvania, crash site" also were taken to an unidentified landfill.

"These cremated portions were then placed in sealed containers that were provided to a biomedical waste disposal contractor," it said.

The report contradicts a 2011 US Air Force account, which said there were no records that showed how remains at Dover were handled before 2003.

Air Force Secretary Michael Donley told a news conference on Tuesday he was not aware that some remains of 9/11 victims had been taken to a landfill, saying: "This is new information to me."

But retired Army general John Abizaid, who led the review, said he had briefed all the armed services on his report's findings.

The coroner in Pennsylvania's Somerset County who oversaw the recovery of remains from hijacked Flight 93, which crashed in Shanksville, told the Pittsburgh Post-Gazette he was surprised to hear that any remains could have been taken to a landfill.

The only remains sent out were taken to a military institute of pathology in Quantico, Virginia for DNA testing, the coroner, Wallace Miller, was quoted as saying.

The review also contained other revelations of botched management at Dover, with some officials raising concerns about problems at the mortuary as early as 2002.

A May 2002 memo referred to worrisome ‘tracking problems’ with remains, and a 2005 investigation confirmed that "human remains were misrouted in a fashion constituting dereliction of duty," according to the report.

In 2006, the remains of victims killed in the crash of a naval training T-29 aircraft were disposed of as "medical waste" instead of a group burial, it said.

The Air Force in 2008 had to pay a $25,000 settlement to the wife of a Marine for "mental anguish and medical costs" due to the loss of the Marine's personal effects, while in 2009 the mortuary faced allegations of "fraud."

Donley said the Air Force had accepted "responsibility and culpability" over the blunders at Dover mortuary but was now working to ensure no more mistakes occur, Donley said.

"Our focus is from here forward," he said.

An investigation last year found "gross mismanagement" at the facility, with body parts lost in two cases and remains of others mishandled. The findings came after three Air Force employees raised alarm bells over the facility and after an independent probe criticized the Air Force for initially punishing the whistle blowers.

The review issued on Tuesday called for bolstering oversight at Dover, restructuring the chain of command overseeing the mortuary, expanding training and hiring more staff members.