Omar Khadr appears in a military court at the U.S. naval prison at Guantanamo Bay, Cuba. (Canadian Press)

Pretrial proceedings for Canadian Omar Khadr got underway in Guantanamo Bay, Cuba, on Wednesday, with the prosecution and defence both wrangling over what witnesses will be allowed to testify before the U.S. military commission hearing the case.

Last-minute instructions on how the commission should proceed had delayed the pretrial process at the U.S. naval prison, where the Toronto-born 23-year-old has been held on terrorism-related charges since 2002.

Khadr's case is the first to be heard by a military commission since U.S. President Barack Obama instituted reforms that are supposed to make the system fairer for defendants.

Obama had initially said he would abandon the commissions altogether but changed his mind after temporarily suspending them within hours of taking office in January 2009.

Rules governing how lawyers and judges are expected to proceed in the military commissions handling cases like Khadr's were not finalized and approved until late Tuesday night, according to CBC's Bill Gillespie, reporting from Cuba.

"The lawyers and the judge down here hadn't even seen [the rules], and even speed-reading overnight they needed more time," Gillespie said.

The military commissions were established in 2006 to try what the U.S. government then termed "unlawful enemy combatants engaged in hostilities against the United States," including al-Qaeda and Taliban operatives.

Plea bargain possible

Meanwhile, Khadr's lawyers continue to discuss a plea deal for their client that could include repatriation to Canada, according to Khadr's lead U.S. lawyer, Barry Coburn.

Khadr's repatriation would be a major part of any plea bargain, said Coburn, who is based in Washington, D.C.

Khadr is charged with murder, conspiracy and support of terrorism. He is accused of tossing a hand grenade that killed a U.S. medic during a battle in Afghanistan near the Pakistani border in 2002.

Confessions 'unreliable': lawyer

Some of the prosecution's key evidence against Khadr is based on confessions Khadr is alleged to have made to military interrogators, including admitting to have thrown the grenade.

Khadr in an interrogation room at the Guantanamo prison during questioning by a Canadian interrogator. The image is from a 2003 surveillance video and was released by his Canadian defence team on July 15, 2008. (Canadian Press)He also told interrogators he planted roadside bombs and that his al-Qaeda boss would give him $1,500 cash for every American he killed.

His lawyers will seek to have those confessions thrown out, claiming Khadr made them only to avoid torture.

"We will argue that many of those statements were derived in conditions that make them unreliable [and] that Omar Khadr was tortured at times in an abusive situation," Dennis Edney, Khadr's Canadian lawyer, told CBC News.

Khadr, then 15, was captured in a firefight in 2002 and turned over to U.S. military interrogators. He claims he was interrogated more than 100 times, sometimes while in painful stress positions or after long periods of sleep deprivation.

The Canadian government has rejected repeated calls by opposition MPs and human rights groups to ask the U.S. government to repatriate Khadr.

With files from The Canadian Press