Davis said earlier this week that he had resigned over a conflict with his superiors on whether information extracted through waterboarding, a controversial interrogation technique that simulates drowning, could be used at the trials.
"My policy as the chief prosecutor for the military commissions at Guantanamo was that evidence derived through waterboarding was off-limits. That should still be our policy," Davis wrote in the New York Times newspaper.
He also alleges that William Haynes, a Pentagon legal adviser, said in August 2005 that any acquittals of suspects at Guantanamo would make the US look bad, calling into question the fairness of the trials.
The Pentagon has denied that Haynes made the remark.
Davis, now head of the Air Force judiciary, told AP he believes "there are some very bad men at Guantanamo and some of them deserve the death penalty."
But he says civilian political appointees have improperly interfered with the work of military prosecutors.
"I think the rules are fair," he said.
"I think the problem is having political appointees injected into the system. They are looking for a political outcome, not justice."
Hamdan could get a life sentence if the tribunal convicts him of conspiracy and supporting terrorism.
His lawyers admit he was a driver for bin Laden, but say he had no significant role in planning or carrying out attacks on the US.
The US holds about 275 men at Guantanamo and plans to prosecute about 80 before military tribunals.
Earlier this month, the Pentagon charged six detainees with murder and war crimes for the September 11 attacks in 2001 and said they could be executed if convicted.