In this March 2003 photo, Khalid Sheikh Mohammed is seen shortly after his capture during a raid in Pakistan. (Associated Press)

The U.S. government plans to put alleged Sept. 11 mastermind Khalid Sheikh Mohammed and four other Guantanamo Bay detainees in Cuba on trial in a federal civilian court in New York City.

Another five detainees, including Toronto-born Omar Khadr, and Abd al-rahim al-Nashiri, a suspect in the bombing of the USS Cole in 2000 that killed 17 U.S. sailors, will face military commissions.

Attorney General Eric Holder confirmed the plan at a Friday morning news conference.

"After eight years of delay, those allegedly responsible for the attacks of September the 11th will finally face justice. They will be brought to New York to answer to their alleged crimes in a courthouse just blocks away from where the twin towers once stood," Holder said.

Holder said prosecutors expect to seek the death penalty in the civilian court cases.

"I have every confidence we can safely hold these trials in New York as we have so many previous terrorist trials," Holder said.

Speaking earlier in Japan, where he is on an official visit, U.S. President Barack Obama said it was a legal and national security issue.

"I am absolutely convinced that Khalid Sheikh Mohammed will be subjected to the most exacting demands of justice," Obama said.

Trying Mohammed and the other detainees in civilian court, instead of a military tribunal, presents several potential hot issues for the U.S. government. The New York case may force the courts to deal with some counter-terrorism tactics, including interrogation tactics such as waterboarding. Mohammed is reported to have been waterboarded — a simulated drowning — 183 times in 2003, before the practice was banned.

Mohammed and the others have not been formally charged in civilian court, so it is not clear when they may be transferred to New York.

Prosecutors in the Southern District of New York, where the civilian trials will be held, have already handled several terrorism trials in recent decades. Attorneys from the Eastern District of Virginia will also assist in the prosecution.

Holder said it has not been determined where the military commissions, where Khadr will be tried, will be held.

Khadr, 23, was captured by U.S. soldiers in Afghanistan in 2002, and is accused of throwing a grenade that killed U.S. soldier Christopher Speer. He has been held at Guantanamo Bay for the past seven years.

Some leaked documents have called into question the Pentagon's murder case against Khadr.

Khadr had been in legal limbo since Obama announced plans to shut down the Guantanamo detention centre and repatriate the detainees. The U.S. government's original plan was to close the detention centre by Jan. 22, but the Obama administration has said it no longer expects to meet that deadline.

Holder said Friday's announcement marked a step forward on the path to close the Guantanamo prison.

While Holder was holding his press conference, the Canadian government's appeal to the Supreme Court of Canada on the handling of Omar Khadr was underway. The government is appealing a lower court ruling that orders Canada to try to repatriate Khadr. The Canadian government would rather he face U.S. justice instead of being brought back.