Khadr, who was 15 when he was captured in Afghanistan in 2002, is charged with killing a US soldier in a grenade attack and wounding another in a fight at an al-Qaeda base.
A video released last year showed Khadr, who is now 22, crying during questioning by CSIS investigators in 2003.
Documents showed that he had been deprived of sleep before an interview with an official from Canada's foreign ministry in 2004.
The spy agency argued that it had no idea whether Khadr had been deprived of sleep or not before it interrogated him in 2003.
But the committee said CSIS had failed to take into account "widespread media reporting on allegations of mistreatment and abuse of detainees in US custody in Afghanistan and Guantanamo Bay."
The resumption of "administrative" military commission hearings at Guantanamo Bay comes as Barack Obama, the US president, continues his push to have the prison camp closed by January 2010.
Trials of detainees have been suspended pending the outcome of an investigation order by Obama into the running of the prison camp.
'Rush to convict'
Monica Villamizar, Al Jazeera's correspondent at the prison, said that prosecutors are keen to convict as many detainees as possible before it is closed.
"Four hearings are expected to go on in the next 48 hours, which shows the urgency to prosecute as many detainees as possible," she said.
Khadr's defence team told the hearing on Wednesday that he did not wish to be represented by military defence lawyers.
"Khadr has been here for seven-and-a-half years. He has basically said that he wants to fire all his defence team, who are American members of the military, and wants to be counselled and represented by Canadian lawyers," Villamizar reported.
Mohammed Kamin, one of the other detainees due to face the hearing did not show up as he preferred to sleep, Villamizar said.
Captured by US forces in Afghanistan in 2003, he is accused of being a paid-up member of al-Qaeda.