Raed Jaser, 35, was granted the pardon in 2009 for uttering threats and fraud convictions from when he was a young man, his lawyer, John Norris, said Thursday.
Federal Court documents show that the Parole Board of Canada decided to revoke Jaser's pardon in July, months after he was charged with three terror offences in the alleged Via plot.
The parole board wrote to Jaser in June saying it was recommending his pardon be revoked and it finalized the decision on July 30.
"It (said) essentially, 'Because of these charges we've concluded that you are no longer of good character and thus not entitled to the pardon any longer,' which in our view is simply absurd," Norris said in an interview.
Norris is asking the Federal Court to overturn the decision, arguing that revoking Jaser's pardon when his new criminal charges have not been proven is an abuse of process.
"It was completely wrong of them legally to reach this conclusion at this stage of the process where these are nothing but allegations," Norris said.
Jaser and Chiheb Esseghaier were arrested in April and accused of plotting to attack a Via train that runs between Toronto and New York City. Police stressed at the time of the arrests that there was no imminent threat to the public.
Jaser was born in the United Arab Emirates, came to Canada in 1993 and became a permanent resident in 2009, the same year he received his pardon.
The federal government has said it will take steps to deny people without status in Canada the possibility of a criminal pardon after reviewing Jaser's case. The office of the public safety minister has said it is unacceptable that inadmissible foreign nationals are able to get criminal record suspensions.
Esseghaier, a PhD student doing doctoral research on nanosensors in Quebec, is facing five charges, including instructing someone to carry out an activity for the benefit of a terrorist group.
If convicted, they could be sentenced to life in prison.
Under the Criminal Records Act, the parole board can revoke a pardon if someone lied to get it, if they are convicted of a new offence or if there is evidence the person "is no longer of good conduct."
Norris is also asking the Federal Court to declare the good conduct section of the act unconstitutional.
"It confers a discretion on the board that seems completely open-ended and unstructured," Norris said. "What exactly does it mean to be of good character or to fail to be of good character? It is simply too vague to meet constitutional standards."
Federal officials have not yet filed a response to Jaser's judicial review application, which was filed late last week.
Jaser and Esseghaier have a judicial pre-trial set for later this month.
A third man, Ahmed Abassi, is facing terrorism charges in the U.S. and prosecutors allege he "radicalized" Esseghaier. American authorities also said Abassi did not support the alleged Via Rail plot and was pushing for a different plan that would contaminate the air or water with bacteria and kill up to 100,000 people.