WASHINGTON — The Obama administration started proceedings for its first Guantanamo Bay military tribunal Wednesday, charging Abd al-Rahim al-Nashiri, a Saudi, as the mastermind in the bombing of the USS Cole.

While prosecutors intend to seek the death penalty, a conviction is not certain because Nashiri was repeatedly subjected by U.S. interrogators to techniques widely considered to be torture.

According to the CIA, the one-time top al-Qaida lieutenant was held for four years at an undisclosed “”black site”” where interrogators water boarded him, placed a handgun beside his head and fired up an electric power drill. They also threatened to harm his family.

A partly unsealed CIA report says Nashiri was one of three captives given “”enhanced interrogation techniques”” as U.S. officials sought to learn of coming terror attacks. Nashiri allegedly was supervising several al-Qaida plots when he was captured in 2002 in the United Arab Emirates and had risen to power in Osama bin Laden’s terror organization.

But the problem for the administration is the Military Commissions Act of 2009, enacted under Obama’s watch, which prohibits using statements taken through torture. “”No evidence obtained by torture or cruel, inhuman or degrading treatment shall be admissible in a military commission,”” said Army Lt. Col. Tanya J. Bradsher, citing the act.

Also complicating the government’s case is that two participants in the 2000 Cole bombing were convicted in Yemen and are in prison there and unavailable for Nashiri’s trial at the U.S. Naval Base on Guantanamo Bay, Cuba.

But a third witness in custody in the United States has described Nashiri’s role in those bombings. And another witness has identified Nashiri as “”an important person in al-Qaida”” and said Nashiri “”helped arrange the USS Cole bombing.””

Navy Lt. Cmdr. Stephen C. Reyes, Nashiri’s defense attorney, said other suspects in pre-Sept. 11, 2001, attacks were sent to U.S. federal courts, including two indicted in New York for the Cole bombing.

“”But here,”” Reyes said, “”the only difference is that Nashiri was tortured. And the government wants to make the evidence of this disappear by sentencing him to death in a makeshift system.””

Nashiri allegedly was “”in charge of the planning and preparation”” for the Cole attack and is specifically charged with committing terrorism, attacking civilians, intentionally causing bodily injury and murder in violation of the law of war.

In addition to the Cole attack, which killed 17 sailors, wounded 40 others and blew a 30-foot by 30-foot hole in the side of the ship, Nashiri also was charged with planning the Oct. 6, 2002, attack on a French civilian oil tanker MV Limberg and planning an attempted attack on the USS The Sullivans as the ship refueled in the Port of Aden on Jan. 3, 2000.

Prosecutors are asking for the death penalty, but their request is subject to approval by the head of the military commission.

Military prosecutors had filed charges against him earlier. But Obama, promising to close the Cuban prison, took office in January 2009 and halted the military tribunal process. A month later the charges were dropped.

In March, Obama announced that the administration would be resuming military trials for terrorism suspects detained at Guantanamo Bay, despite his 2008 campaign promise to close the prison.

Nashiri acknowledged in a 2007 Guantanamo Bay hearing that he helped obtain the small boat that carried explosives to the Cole. But he said he gave it to a businessman for a fishing trip, and did not know it would be used by suicide bombers. “”I had nothing to do with these people,”” he said.

He also spoke of the pain he was subjected to. “”From the time I was arrested, they have been torturing me. One time they tortured me one way and another time they tortured me in a different way. … They do so many things.””

He specifically described water boarding — “”they used to drown me in water.”” To get them to stop, Nashiri said, he would “”invent”” stories, even saying bin Laden had a nuclear bomb.

The CIA report said Nashiri’s torture began upon his arrival at the black site. “”Nashiri provided lead information on other terrorists during his first day of interrogation,”” the report said.

By the 12th day, he had been water boarded twice. He also was kept in stress positions, pulled around his cell, and left naked and hooded. If he did not cooperate, he was warned, “”we could get your mother in here. … We can bring your family in here.””