The claim comes in material filed late Monday as part of Ottawa's 11th-hour attempt to block Khadr's release from prison — which could come as early as Tuesday.
"A lack of clarity in the international transfer process may jeopardize the system as a whole," the government said in documents obtained by The Canadian Press.
"(Khadr's) release unsettles the foundation of this system by introducing uncertainty and a lack of control over the manner in which Canadian offenders' sentences are enforced."
Despite having presented no such evidence at his bail hearing, the government now argues that allowing Khadr out — given his long incarceration — presents a risk that is contrary to the public interest.
"Springing (him) into the community rather than allowing him to continue his planned reintegration poses an undue risk," the government states.
It does not elaborate on the nature of the risk but notes Khadr has applied for parole in June.
On Monday, the government also filed its formal notice of appeal of the April 24 decision by Justice June Ross of the Alberta Court of Queen's Bench granting Khadr bail. It wants the stay pending disposition of the case.
The last-ditch stay application, slated to be heard by a single Court of Appeal justice on Tuesday morning, says the government "will suffer irreparable harm" if the Toronto-born Khadr, now 28, is released.
Ottawa maintains that Ross had no jurisdiction to hear Khadr's bail application under the provisions of the International Transfer of Offenders Act — the treaty that saw him returned to Canada from Guantanamo Bay in September 2012 to serve out his eight-year sentence for five war crimes.
Allowing him out on bail — an unprecedented situation — could jeopardize the repatriation of other Canadian prisoners and damage Canada's relations with the U.S., the government said.
But a spokeswoman for the U.S. State Department said in a statement Monday the decision to grant Khadr bail will not harm relations between the two countries.
"The United States has a close and co-operative relationship with the Government of Canada," the statement said. "We maintain continuous discussions on a broad range of issues, including security."
The federal government aruges that Ross gave "short shrift" to Canada's "real and consequential" international obligations and was wrong to find that the right to seek bail pending appeal is a constitutionally guaranteed "principle of fundamental justice."
The justice was also wrong to accept Khadr's submissions that his appeal in the U.S. against his war crimes conviction has real merit and a strong chance of success.
Public Safety Minister Steven Blaney said on Monday the government has been consistent in its approach to Khadr — which has been to brand him as an unrepentant terrorist.
"We feel that Mr. Khadr, until a final decision is rendered by the court, should stay behind bars," Blaney said in Ottawa.
In 2010, the Toronto-born Khadr pleaded guilty to five war crimes — including murder for the death of an American special forces soldier — before a widely discredited U.S. military commission. The alleged offences occurred in Afghanistan in July 2002 when he was 15 years old.
He later said he only pleaded guilty to get out of Guantanamo Bay because the Americans could have held him indefinitely even if he had been acquitted. He is serving his sentence in Bowden Institution, near Innisfail, Alta.
In a statement, a Khadr support group denounced the government's "unrelenting vilification" of the prisoner and its "knee-jerk" appeal of every court decision favourable to him.
"The rights, freedom and liberties of all Canadians are diminished by the actions of this government," Free Omar Khadr Now said.