An FBI agent’s claim that Omar Khadr had seen Maher Arar at terrorist “safe houses” in Afghanistan was severely undermined today when a military court was told that Arar was in North America during the time in question.

FBI Special Agent Robert Fuller testified Monday that Khadr said he recognized a photo of Arar during an October 2002 interrogation.

Under questioning Tuesday, Fuller said Khadr saw Arar in Afghanistan during late September or October 2001.

A Canadian judicial inquiry determined in 2006 that Arar was working in San Diego on a business trip on the day of the 9/11 terror attacks — and back in Canada in October. In fact, Arar first drew the interest of the RCMP when he met another man they were watching in an Ottawa cafe Oct. 12, 2001.

The FBI claim has drawn ire in Canada and in Ottawa Tuesday Foreign Affairs Minister Lawrence Cannon said the government has not been shaken from its belief that Arar is an innocent man.

Arar has denied ever being in Afghanistan.

Fuller’s evidence was further undercut by revelations that the FBI notes taken during the interrogation stated Khadr was shown a photograph of Arar and at first said he “looked familiar.” The notes recorded that “in time” Khadr stated “he felt he had seen” Arar.

Tuesday’s pre-trial hearing was cut short after only two hours so Guantanamo’s military personnel could watch the televised swearing in of their new commander-in-chief. Photos of former president George W. Bush on the U.S. naval base were replaced with framed pictures of Barack Obama shortly after his inauguration.

That’s not all that’s expected to change.

Obama has vowed to shut Guantanamo’s prison and there’s speculation he will halt the military trials where Khadr is charged with killing a U.S. soldier and four war crimes.

Khadr’s lawyers had tried repeatedly to have this week’s hearing delayed so as not to end on the government’s evidence if Obama stops the trial.

Cannon stood by the results of the Canadian inquiry in which Justice Dennis O’Connor concluded Arar was a wronged man.

“Justice O’Connor did a fulsome report ... (and) the government acknowledged and accepted its recommendations,” Cannon told the Star.

Arar was awarded $10.5 million in compensation and an apology from Prime Minister Stephen Harper following the federal inquiry that revealed the RCMP had passed erroneous information connecting Arar to terrorism to their U.S. counterparts.

NDP critic Joe Comartin said the security and intelligence agencies involved in the Arar and Khadr cases continually “try and cover themselves even when the evidence is overwhelmingly the other way. If you told a story once, you have to keep telling it.”

Arar himself declined requests Tuesday for comment.

Kerry Pither, Arar’s former spokesperson, and the author of Dark Days about the arrest and torture of Arar and three other Canadians in Syria, condemned the FBI for “gratuitously smearing” Arar in the final days of the Bush administration.

“Who benefits from this? The people and the officials who benefit are those who are implicated in Maher Arar’s rendition and torture in Syria, and that includes the FBI, the CIA, CSIS and the RCMP.”

Paul Cavalluzzo, the commission counsel to Justice O’Connor, noted that the report concluded there was no evidence Arar was engaged in terrorist activity.

Cavalluzzo said that “given what’s happening at Guantanamo Bay, it wouldn’t surprise me if it was a product of torture, which means that it’s meaningless and useless information.”

Navy Lt.-Cmdr. Billl Kuebler, Khadr’s Pentagon-appointed lawyer said Tuesday outside court that Khadr, who was 15 and gravely injured when he arrived at the U.S. base in Bagram, would have “confessed to seeing the Pope,” to make his interrogations stop.

Military interrogators questioned Khadr more than 40 times at Bagram before FBI agent Fuller questioned him. Some of those Bagram interrogators were later convicted for the death of an innocent Afghan taxi driver.

The timing of Khadr’s interrogation with Fuller is also revealing.

Arar was arrested at JFK airport in late September 2002 en route back to Canada from a family holiday and held for two weeks before being rendered to Syria Oct. 8 - one day after Khadr’s interrogation began.

Khadr, now 22, was scheduled to go on trial Monday but Army Col. Patrick Parrish, the military judge presiding over the case, said he would set a new date because pre-trial hearings would not be completed by Friday.

Parrish said the case resumes Wednesday morning unless he is “otherwise ordered.”

With files from Richard Brennan