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Raed Jaser, 35, is brought into Toronto’s Old City Hall court building in the back of an RCMP cruiser on April 23, 2013.PETER POWER/The Globe and Mail

Federal officials have revoked a pardon that was granted years ago to a man who now stands accused of an "al-Qaeda-inspired" plot to kill train passengers crossing the Canada-U.S. border.

Raed Jaser, a 35-year-old who had arrived in Toronto as an asylum seeker, has been jailed on terrorism charges since April in connection with an alleged plot to derail a train travelling from New York. While his guilt or innocence in the case has not been determined, he has already raised flags within government for lingering in Canada, without status, for years after he was convicted of more minor offences.

New court filings show that, in 2009, Mr. Jaser received a pardon for past crimes, which include fraud and uttering threats. Then, this past July, Parole Board of Canada officials wrote to him in prison to say that they were revoking the pardon because he is no longer considered to be "of good conduct."

Official statistics indicate that pardons are rarely revoked in Canada – only about 3 or 4 per cent of the time. Last week, a lawyer acting for Mr. Jaser filed a Federal Court lawsuit, seeking to reverse the revocation and calling it "contrary to law and the principles of fundamental justice."

In April, Mr. Jaser, Chiheb Esseghaier and Ahmed Abassi, were respectively arrested in Toronto, Montreal and New York as cogs in an alleged international conspiracy to attack an Amtrak-Via train as it crossed the border. Police have alleged that shadowy al-Qaeda figures based in Iran helped cook up the scheme.

In the immediate aftermath of the busts, it was revealed that federal officials had spent years trying to kick out Mr. Jaser, long before he was considered a terrorism suspect. Then-immigration minister Jason Kenney vowed to tighten certain loopholes that were seen to have allowed him to remain in Canada.

Since arriving 20 years ago as a refugee claimant, the Palestinian born in the United Arab Emirates frequently found himself in trouble with the law. During the 1990s and in 2000, Mr. Jaser was convicted on several counts of fraud and also of uttering threats.

These crimes were invoked by government lawyers in 2004, as a tribunal ruled that Mr. Jaser was a bogus refugee who should not be allowed to stay in Canada. He still managed to resist deportation by countering that he was a "stateless Palestinian" who had had no motherland to return to.

In 2009, Mr. Jaser won his bid for a pardon, a act of government clemency that apparently allowed him to better pursue permanent resident status, which was also granted to him in that year.

Mr. Jaser had filed his pardon application before the Conservatives passed a 2012 law that tightened the rules. Those changes followed a scandal where it was revealed that Graham James, a hockey coach who sexually assaulted boys, had himself gotten a pardon.

Last year, police pegged Mr. Jaser as a terrorism suspect as RCMP and U.S. Federal Bureau of Investigation detectives teamed up over several months to pursue suspects on both sides of the border.

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