Khalid Sheikh Mohammed, the self-described mastermind of the terrorist attacks of September 11, 2001, and four other men accused in the plot will be prosecuted in federal court in New York City, the United States attorney general announced on Friday.

But the administration will prosecute another set of high-profile detainees now being held at the military prison at Guantánamo Bay, Cuba — Abd al-Rahim al-Nashiri, who is accused of planning the 2000 bombing of the Navy destroyer Cole in Yemen, and four other detainees — before a military commission.

Attorney General Eric H Holder Jr announced those decisions in a news conference on Friday at the Department of Justice. The arrangements would mean that civilian prosecutors would handle those detainees accused of the 2001 terrorist attacks, which killed nearly 3,000 people in New York, northern Virginia and Pennsylvania, while the 2000 attack against the Cole would remain within the military system.

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

The decision marks a milestone in the administration’s efforts to close the Guantánamo prison, something that President Obama announced shortly after taking office that he would do within a year, but that has proved difficult to achieve because of uncertainty about what to do with the detainees housed there.

Obama, asked about the decision in a news conference on his trip to Asia, declined to comment directly, but said that Mohammed would face justice.

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