Canadian Omar Khadr was 15 when he was captured
Guantanamo Bay interrogators were told to destroy handwritten notes in case they were called to testify on detainee treatment, a military lawyer alleges.
The lawyer, Lt-Cmdr William Kuebler, said the instructions were contained in a Pentagon operations manual.
He said this apparent destruction of evidence at the prison camp stopped him from challenging alleged confessions in the case of his client, Omar Khadr.
He would use the document to seek a dismissal of the charges, he said.
Mr Khadr - a Canadian - is the only Westerner still held at the jail.
The 21-year-old is accused of killing a US soldier and wounding another during a battle in Afghanistan in 2002.
Mr Khadr was 15 when he was captured during the firefight at a suspected al-Qaeda camp in Afghanistan.
He faces a maximum sentence of life in prison if convicted.
Two weeks ago, Canada's Supreme Court ruled the Canadian government had acted illegally by handing over documents from an interview with the suspect by its own intelligence services a year after his capture.
'Crucial to the case'
The manual on "Standard Operating Procedures" which reportedly contained the instructions was obtained by Lt-Cmdr Kuebler from prosecutors last week as part of a pre-trial review of evidence, he said.
The lawyer said the evidence was crucial to the case as prosecutors were relying on evidence extracted at Afghanistan's Bagram air base and Guantanamo.
"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," Lt-Cmdr Kuebler quoted the document as saying in a signed affidavit.
Correspondents say the document could support challenges by other detainees to the use of confessions as evidence.
Last week the trial by military tribunal of five Guantanamo inmates began at the camp. They face charges relating to the 9/11 attacks on the US.
The trials have already raised questions about not just the treatment of detainees, but also the legitimacy of American military commissions.
Later this month, the US Supreme Court is to rule on the rights of prisoners being held at Guantanamo Bay, threatening a possible delay or even halt to the proceedings.