Omar Khadr is shown appearing earlier in a military court at the U.S. naval prison at Guantanamo Bay, Cuba.

Canadian Omar Khadr showed up at the afternoon portion of his pretrial hearing at Guantanamo Bay on Thursday after refusing to go in the morning, but he did so in "extreme pain," his lawyers said.

Toronto-born Khadr, who is accused by the United States of murder, conspiracy and supporting terrorism in the Afghan war, didn't attend the morning proceedings of his military trial because he was asked to wear blackout goggles and earmuffs on the way to court.

The guards at the U.S. naval base in Cuba wanted to prevent him from seeing and hearing while he was being transported in a secure van, something Khadr's lawyer said he's never been required to do before.

Khadr refused to wear the eye and ear coverings, saying they were meant to humiliate him. The guards refused to move him to court without the headgear.

Col. Patrick Parrish, the military judge in charge of the pretrial proceedings, postponed the hearing until the afternoon but said it could proceed without Khadr if necessary.

Khadr's lawyers, having been instructed by Parrish to talk to their client, had the 23-year-old brought back to the tribunal for the afternoon session, but Khadr, who is blind in his left eye, appeared to be suffering.

Khadr had received medical treatment earlier in the morning for an outbreak of conjunctivitis, an eye inflammation, his lawyers said.

"He's sitting there at the bench, slumped. He's got his hands over his eyes, he's wiping his eyes with tissue," the CBC's Bill Gillespie reported from Guantanamo Bay. "And his lawyers are saying ... he's in extreme pain."

Parrish ordered that the case proceed, and the tribunal heard from an FBI agent who had interrogated Khadr.

Khadr is accused of tossing a hand grenade that killed a U.S. medic during a battle in Afghanistan near the Pakistani border in 2002.

Defence rejects plea offer

His defence team has already rejected a plea-bargain offer from U.S. military prosecutors that would have forced him to serve a sentence in a U.S. prison, one of his lawyers said.

"It was 13 years that was offered," Dennis Edney, Khadr's Canadian lawyer, told CBC News. "Time served and Mr. Khadr would spend five years in a maximum-security prison in the United States."

Edney, who declined to explain exactly why the defence didn't accept the offer, said part of the problem was that it would have required Khadr to serve the rest of his sentence in the U.S., instead of Canada.

"I'm prepared to consider anything that brings Omar Khadr back to Canada," Edney said.

Khadr has been imprisoned at Guantanamo Bay since he was arrested in Afghanistan at age 15. He is facing a possible life sentence if convicted. Human rights groups have decried his detention because international law requires combatants under age 18 to be treated as child soldiers and as victims in need of rehabilitation and reintegration.

Washington-based lawyer Barry Coburn, who is leading Khadr's defence team at Guantanamo Bay, confirmed that lawyers were discussing plea bargains.

He said the prosecution is insisting that Khadr publicly admit he threw the grenade that killed an American soldier in Afghanistan as part of any possible plea — something Khadr won't do, Coburn said.

New rules released

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.

The military commission manual, implementing laws enacted by the Obama administration last year, was only made available to counsel at Guantanamo Bay on Tuesday evening.

The manual is important to Khadr's defence team, since the pretrial proceedings this week centre on whether self-incriminating statements will be admissible at his trial.

The defence said it will seek to have the confessions thrown out, arguing that Khadr made the statements only to avoid torture.

The prosecution, on the other hand, insists Khadr's claims of torture are baseless and self-serving, and that the various statements should be allowed as evidence.

A number of military interrogators who interviewed Khadr after he was captured are scheduled to appear at the hearing in the coming days.

The new rules also make explicit a new Pentagon policy that even if a prisoner is acquitted at a Guantanamo military tribunal, they can still be detained indefinitely.