Prime Minister Stephen Harper said Monday that Omar Khadr's return to Canada is far from guaranteed, after president-elect Barack Obama announced he will issue an executive order to shut down the prison at Guantanamo Bay.

Toronto-born Khadr, 22, is charged with killing a U.S. soldier in Afghanistan when he was 15 -- a child soldier, according to his Pentagon lawyer, Lt.-Cmdr. Bill Kuebler.

Harper said the fact Khadr has been charged with a crime may suggest he will remain in U.S. military custody after the prison in Guantanamo, a navy base in Cuba, is closed

"The promise that president-elect Obama made was that he would close down the facilities at Guantanamo. That's primarily, as I understand it, because of the objection to the fact that many of the people at that facility aren't charged with anything," he told reporters in Vancouver.

"I don't think you can necessarily leap to the conclusion that it will affect people who have in fact been charged, and who are facing a legal process. We don't know the answer to that question."

But Kuebler said Obama's order may also involve ending the military commissions at the prison, whether or not the inmates have been charged.

"I can't imagine the president is going to sign an executive order that would not also stop the military commission process," he said on CTV Newsnet's On the Hill.

"It would be extremely inconsistent if on day one he signed an executive order saying that Guantanamo is an affront to the rule of law and he wanted to shut it down, and then on day six, he was the first president in U.S. history to preside over the trial of a child for war crimes by military tribunal. So I fully expect the trial process to stop."

Obama may issue the order as soon as he takes office. That may be as early as Jan. 20, his inauguration date, according to an advisor who spoke to the The Associated Press.

It's believed around 250 al Qaeda members are being held at Guantanamo. That includes 15 "high value detainees," considered by U.S. official to be extremely dangerous. If the prison is closed, it's unclear where these inmates would be placed, or what sort of legal process they would enter.

Also, detainees held on U.S. soil have certain legal rights that Guantanamo's inmates lack.

Those problems suggest it will take up to 100 days, or perhaps longer, to carry out the order.

Obama acknowledged the potential difficulties Sunday during an interview with ABC's "This Week."

"I think it's going to take some time and our legal teams are working in consultation with our national security apparatus as we speak to help design exactly what we need to do.

"But I don't want to be ambiguous about this," he said. "We are going to close Guantanamo and we are going to make sure that the procedures we set up are ones that abide by our constitution."

The navy base at Guantanamo dates back to 1903, and has remained in operation since Fidel Castro took power in Cuba in 1959. Less than one month after the Sept. 11, 2001 terrorist attacks, hundreds of terrorist suspects were brought to the prison, and in 2002 it became the main detention centre used in the so-called war on terror.