By David Alexander

WASHINGTON (Reuters) - Cremated remains that may have included those of victims of the September 11 attacks were incinerated and sent to a landfill despite an internal debate in which some officials at the main U.S. military mortuary recommended the ashes be dispersed at sea.

Documents released on Friday show that nearly one year after the September 11, 2001 attacks, military and civilian personnel responsible for the mortuary at Dover Air Force Base in Delaware engaged in an lengthy e-mail exchange over what to do with 1,321 portions of remains.

The fragmentary remains, which were categorized as "Group F," were unidentified and could not be linked to any specific victim of the September 11 attack on the Pentagon.

They were mixed in with debris from the building and airplane, and could have included remains of the hijackers as well, an official said on Friday, adding that it was not even certain they were human.

"They could have been anything biological. So there may have been human, but it could have been something from someone's lunch, anything that would be of a biological nature," said Jo Ann Rooney, acting undersecretary of defense for personnel and readiness.

Navy Captain Craig Mallak, the Dover medical examiner, said the mortuary encourages workers at the scene of a mass disaster to collect anything they think might be a sample that would help to identify a victim. He said thousands of unidentified samples sometimes remain at the end of an investigation.

The Pentagon released about 2,000 pages of documents on Friday that were gathered as part of an investigation into allegations that the Dover mortuary mishandled the remains of war dead. That investigation revealed that some remains from September 11 had been incinerated and sent to a landfill.

The discovery raised concerns among the families of the September 11 victims. Rooney said she had met with representatives of the families on Friday to assure them the bodies of their loved ones had been treated with dignity and respect.

But an e-mail among the released documents showed that many officers who debated how to dispose of the Group F remains believed they should have been treated as if they belonged to the victims of the September 11 attack.

One military officer suggested that once remains were cremated, the ashes should be dispersed at sea. His name, like all others in the e-mail exchange, were redacted.

Another officer agreed and suggested, "it may be appropriate for us to witness and perhaps even have a chaplain present."

"I do like the idea of spreading the ashes at sea in that it's a neutral arena, it should represent an area readily agreeable to all parties," a colonel added.

But another, evidently senior, official objected, saying the remains being disposed of were considered "medical waste" and the contractor responsible for the cremation "should not return any medical waste back to the military service."

"Powder and ashes from the incineration of the material and the containers that were used for the burning is to be disposed of as normal waste," the official wrote.

"We shouldn't attempt to spread the residue at sea, as it could possible (sic) send a message to the next of kins (sic) that we are disposing human remains, and that is not the case," the official wrote. "Please have the contractor responsible for the incineration 'immediately' dispose of all residual materials."

A colonel agreed to do as directed, saying he assumed headquarters had been consulted, but he noted: "My point, as you are aware, is that Group F is not your normal set of medical waste."

The official replied "understand Group F was special," but added that the decision had been coordinated with other senior officials responsible for the mortuary.

The colonel then agreed to do as directed and forwarded the e-mail to another colonel, saying: "Dispose of Group F as stated and keep this email as proof of our coordination."

The practice of incinerating partial remains as "medical waste" and disposing of them in a landfill was discontinued in 2008. They are now buried at sea.

(Reporting By David Alexander; Editing by Stacey Joyce)