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 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 angered military families and led to a new policy.
Starting in 2008, the military decided to dispose of unidentified cremated remains at sea.
But the review released 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.
Details about the 9/11 remains were mentioned in passing as background material in the report, which focused on how to fix management problems at the troubled mortuary.
Retired Army general John Abizaid, who led the review, told reporters it was unclear how many partial remains of September 11 victims were involved.
"I don't know that there's a way to find out," he told reporters.
Air Force Secretary Michael Donley later on Tuesday said 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 Abizaid 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.
"Where they would have gotten those remains I have no idea," Wallace Miller was quoted as saying. The only remains sent out were taken to a military institute of pathology in Quantico, Virginia for DNA testing, he said.
The review also contained other revelations of botched management at Dover, with 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 allegeations 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 Tuesday called for bolstering oversight at Dover, restructuring the chain of command overseeing the mortuary, expanding training and hiring more staff members.
It remained unclear Tuesday if the Air Force would sack any of those responsible for the errors at Dover.