Published: Friday, 13 Nov 2009 | 8:33 AM ET

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Khalid Shaikh Mohammed, the self-described mastermind of the Sept. 11 attacks, and four other men accused in the plot will be prosecuted in federal court in New York City, a federal law enforcement official said early on Friday.

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But the administration will prosecute Abd al-Rahim al-Nashiri — the detainee accused of planning the 2000 bombing of the U.S.S. Cole in Yemen — and several other detainees before a military commission, the official said.

The decisions to give civilian prosecutors detainees accused of the 2001 terrorist attacks and keep the case of the Cole attack within the military system are expected to be announced at the Department of Justice later on Friday by Attorney General Eric H. Holder Jr. The official spoke on condition of anonymity because that news conference has not yet taken place.

The decision about how to try several of the most high-profile detainees at Guantánamo marks a milestone in the administration’s efforts to close the facility, a policy that President Obama announced shortly after taking office but which has proven more difficult than his team anticipated.

No detainee is being moved right away. Under a law Congress enacted earlier this year, lawmakers must be given 45 days advance notice before the executive branch moves a Guantánamo detainee onto United States soil.

The decisions about how to prosecute Mr. Mohammed and Mr. Nashiri have been particularly difficult because their defense lawyers are expected to argue that they were illegally tortured by the Central Intelligence Agency during their confinement, tainting any evidence gathered from their interrogations.

Documents have shown that the CIA used waterboarding — a controlled drowning technique — against Mr. Mohammed 183 times in March 2003. Mr. Nashiri is one of two other detainees known to have been waterboarded before the Bush administration shut down the program, which high-level officials had approved after the Justice Department wrote legal memorandums arguing that the president, as commander-in-chief, could authorize interrogators to bypass anti-torture laws.

In other cases in which the administration has discussed transferring detainees, local communities have risen up through political leaders to say they did not want the prisoners because their towns could become a target for terrorism.

New York City has been different. In March, for example, when the administration prepared to bring Ahmed Kahlfan Ghailani, a suspect in the 1998 bombings of United States embassies in Africa which killed 224 people, to face trial there, Senator Charles Schumer, Democrat of New York, reacted with equanimity, saying that the city was well-accustomed to handling high-profile terror suspects, cit

“Bottom line is we have had terrorists housed in New York before,” Mr. Schumer said at a March news conference at the Capitol with other Democratic leaders. “They’ve been housed safely.”

Mr. Schumer at the time pointed to the “blind sheikh” Omar Abdel Rahman, convicted in connection with the 1993 World Trade Center bombing, as an example. “The main concern is bringing these terrorists to justice and making sure the public is safe,” Mr. Schumer said. “I have faith that the administration will do both.”

Still, Mr. Ghailani is not facing a potential death sentence, and is not nearly as high profile as Mr. Mohammed. A Sept. 11 plot prosecution in New York City could test such attitudes.

Mr. Mohammed and the four other suspects accused of helping organize the Sept. 11 plot — Ali Abd al-Aziz Ali, Waleed bin Attash, Ramzi Binalshibh, and Mustafa Ahmad al-Hawsawi — had been facing potential death sentences if convicted of the charges the Bush administration had brought against them in military commissions before the Obama administration froze those proceedings. It was not clear what charges they would now face in civilian court.

It was not immediately clear where the military commission trials would take place. The Bush administration spent tens of millions of dollars on a commissions courtroom at Guantánamo, but it has sat empty since the Obama administration froze legal proceedings there to undertake a review of how to handle the detainees. Officials have been eyeing military brigs elsewhere, including some inside the United States.

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