Interrogators at Guantánamo Bay were told to destroy their notes to stop them potentially being used to highlight the mistreatment of detainees, according to a US military lawyer.

William Kuebler, a lieutenant commander who is defending Omar Khadr, a Canadian national facing trial for alleged war crimes in Afghanistan, said the classified instructions were included in an operations manual that prosecutors allowed him to see last week.

The apparently wilful and officially sanctioned destruction of notes meant he would be unable to challenge supposed confessions given by Khadr, Kuebler said yesterday.

He told reporters the instruction was contained in a US military manual of standard operating procedures, or SOPs, for interrogators that was shown to him during a pre-trial review of possible evidence.

"The mission has legal and political issues that may lead to interrogators being called to testify … Keeping the number of documents with interrogation information to a minimum can minimise certain legal issues," the document was cited as saying in an affidavit signed by Kuebler.

The navy lawyer now plans to seek a dismissal of charges against 21-year-old Khadr, who was detained in Afghanistan at the age of 15.

Khadr, who faces a series of charges, including murder for allegedly throwing a grenade that killed a US special forces soldier in 2002, is set to be one of the first Guantánamo detainees to face a war crimes trial.

Kuebler said the way the interrogations were carried out was central to Khadr's case because prosecutors were relying largely on testimony obtained from him at Guantánamo, and earlier at Bagram air base, in Afghanistan.

"If handwritten notes were destroyed in accordance with the SOP, the government intentionally deprived Omar's lawyers of key evidence with which to challenge the reliability of his statements," Kuebler said.

Prisoners released from both Guantánamo and Bagram have alleged routine mistreatment during interrogation. The Pentagon denies this.

Kuebler said the operations manual, from January 2003, was attached to a 2005 report into alleged detainee abuse at Guantánamo, but that the section covering the manual was not made public at the time.

The 2005 report documented degrading treatment, but stopped short of saying torture occurred.

At the weekend, the Pentagon said the process of trying Guantánamo prisoners for alleged war crimes was a "number one priority". It said it was doubling the total of military lawyers assigned to prosecution and defence teams. About 270 detainees remain at the former naval base, of which the US military hopes to prosecute up to 80.

Critics of the hearings say the US is seeking to rush through trials before the presidential election in November. However, claims that potential evidence was destroyed could be used by lawyers defending other detainees to challenge their alleged confessions.