A document obtained and witnesses interviewed by Fox News raise new questions over whether there was an effort by the Defense Department to cover up a pre-9/11 military intelligence program known as "Able Danger."

At least five witnesses questioned by the Defense Department's Inspector General told Fox News that their statements were distorted by investigators in the final IG's report -- or it left out key information, backing up assertions that lead hijacker Mohammed Atta was identified a year before 9/11.

Atta is believed to have been the ringleader of the Sept. 11 hijackers who piloted American Airlines Flight 11 into the World Trade Center. Claims about how early Atta first tripped the radar of the Department of Defense date back to 2005, but those claims never made it into the Inspector General's report. The report was completed in 2006 and, until now, has been available only in a version with the names of virtually all of the witnesses blacked out.

Fox News, as part of an ongoing investigation, exclusively obtained a clean copy of the report and spoke to several principal witnesses, including an intelligence and data collector who asked that she not be named.

The witness told Fox News she was interviewed twice by a Defense Department investigator. She said she told the investigator that it was highly likely a department database included the picture of Atta, whom she knew under an alias, Mohammed el-Sayed.

"When it came to the picture, (the investigator) he was fairly hostile," the witness told Fox News. She said it seemed the investigator just didn't want to hear it. "Meaning that he'd ask the same question over and over again, and, you know, you get to the point you go, well, you know... it's the same question, it's the same answer."

The IG report didn't accurately reflect her statements to investigators, she said, adding that she doesn't think the investigator simply misunderstood her.

Lt. Col Tony Shaffer, an operative involved with Able Danger, said he was interviewed three times by Defense investigators. He claims it was an effort to wear down the witnesses and intimidate them. Two other witnesses, one a military contractor and the other a retired military officer, said they had the same experience. The two witnesses spoke to Fox News on the condition of anonymity because they said they feared retaliation. A fifth witness told Fox that statements to investigators were ignored.

"My last interview was very, very hostile," Shaffer told Fox News last month before he was ordered by the department not to discuss portions of his book, "Operation Dark Heart," which included a chapter on the Able Danger data mining project.

When asked why the IG's report was so aggressive in its denials of his claims and those of other witnesses -- that the data mining project had identified Atta as a threat to the U.S. before 9/11 -- Shaffer said Defense Department was worried about taking some of the blame for 9/11.

However, It still isn't clear how -- or whether -- the information on Atta could have been used to the disrupt the Sept. 11 attacks.

"The big picture was not Atta, not so much the chart," Shaffer said. "The fact is this: That we had a pre-9/11 Department of Defense operation focused on taking action against Al Qaeda globally."

Specifically, the Defense Intelligence Agency or DIA wanted the removal of references to a meeting between Shaffer and the executive director of the 9/11 Commission, Philip Zelikow, removed. Shaffer alleges that in that meeting, which took place in Afghanistan, the commission was told about Able Danger and the identification of Atta before the attacks. Shaffer, who was undercover at the time, said there was "stunned silence" at the meeting.

No mention of this was made in the final 9/11 Commission report.

"Dr. Philip Zelikow approached me in the corner of the room. 'What you said today is very important. I need you to get in touch with me as soon as you return from your deployment here in Afghanistan,'" Shaffer said.

Once back in the U.S., Shaffer says he contacted the commission, but without explanation, the commission was no longer interested.

Last month, the Defense Department took the highly unusual step of buying and destroying 9,500 copies of Shaffer's book "Operation Dark Heart" at a cost of $47,000 to U.S. taxpayers.

Click here to see Defense Intelligence Agency, or DIA, letter objecting to parts of the book.

When asked whether Defense Department stood behind the IG report's findings, Col. Dave Lapan, the acting deputy assistant Secretary of Defense said in a statement to Fox News dated Oct. 6, "The investigation found that prior to September 11, 2001, Able Danger team members did not identify Mohammed Atta or any other 9/11 hijacker. While four witnesses claimed to have seen a chart depicting Mohammed Atta and possibly other hijackers or "cells" involved in 9/11, the investigation determined that their recollections were not accurate."

As for retaliation against Shaffer who said he lost his security clearance as a result of speaking out about Able Danger, Lapan said "The investigation found that DIA officials did not reprise against LTC Shaffer, in either his civilian or military capacity, for making disclosures regarding Able Danger or, in a separate matter, for his earlier disclosure to the DIA IG regarding alleged misconduct by DIA officials that was unrelated to Able Danger."

Separately, Fox News has obtained a letter that challenges the Defense Department's claim. In October 2006, then Rep. Christopher Shays, chairman of the Subcommittee on National Security, Emerging Threats and International Relations, wrote to Shaffer's supervisor, Maj. Gen. Elbert Perkins, about the revocation of his clearance..

"Based on investigation of security clearance retaliation, it appears the Defense Intelligence Agency (DIA) used the security clearance system in an improper manner against LTC Shaffer and did not follow DOD security clearance guidelines," Shays, R-Conn., wrote.

Click here to se Shays' letter to Perkins.

In this case, the letter stated that the allegations used by the DIA to justify pulling Shaffer's security clearance included "the alleged misuse of a government cell phone in the amount of $67.00 and the alleged misfiling of a travel voucher for $180.00...these were not uniformed code of military justice (UCMJ) issues -- that there was no basis for punitive action and should be dealt with administratively...This decision cleared the way for LTC Shaffer's promotion, and his current 'good' standing in the Army Reserve.."

This investigation is part of an ongoing series, "Fox News Reporting.” Earlier this year, the series special "The American Terrorist" uncovered new details about the American cleric Anwar al-Awlaki, who is linked to the attempted Christmas Day bombing, and about efforts by the FBI to track and recruit him for intelligence purposes after 9/11.