GUANTÁNAMO BAY, Cuba, Nov. 8 — The administration’s problem-plagued military commission system started up here again Thursday, but it began with contentious new claims that the war crimes cases are unfairly stacked against detainees.

Military defense lawyers said that on the eve of the hearing, military prosecutors told them for the first time of a government witness who might be able to help a detainee, Omar Ahmed Khadr, counter the war crimes charges on which he was arraigned Thursday.

Mr. Khadr, the only Canadian detainee at Guantánamo, has been held here since he was 16. He is now 21.

“It is an eyewitness the government has always known about,” said Lt. Cmdr. William C. Kuebler of the Navy, Mr. Khadr’s chief military lawyer, who questioned why the military was only now informing the defense. Mr. Khadr is charged with the murder of an American soldier, spying, material support for terrorism and other charges.