A senior military legal official approved non-capital charges that include conspiracy, murder and terrorism for the men, who have been in US custody for 17 years for their alleged roles in the deadly bombing of Bali nightclubs in 2002 and a year later of a JW Marriott Hotel in Jakarta.

The timing of the charges, which were submitted under president Donald Trump but not finalised, caught lawyers for the men by surprise.

"The timing here is obvious, one day after the inauguration," said Marine Corps Major James Valentine, the military lawyer for the most prominent of the three. "This was done in a state of panic before the new administration could get settled."

A spokesman for the military commissions, which have been bogged down for years over legal challenges largely over the brutal treatment of men during their previous confinement in CIA facilities, had no immediate comment.

Military prosecutors filed charges against Encep Nurjaman, an Indonesian known as Hambali, and the other two men in June 2017. The case was rejected by the Pentagon legal official known as a convening authority for reasons not publicly known.

Now the convening authority has approved charges, the US must arraign the prisoners before the military commission at the base in Cuba. The pandemic has halted court proceedings at Guantanamo and it is not clear when they will resume.

Hambali is alleged to have been the leader of Jemaah Islamiyah, a Southeast Asian affiliate of al-Qaeda. The Pentagon said he was accused with Mohammed Nazir Bin Lep and Mohammed Farik Bin Amin, from Malaysia, of planning and aiding the attacks.

All three were captured in Thailand in 2003 and held in CIA custody before they were taken to Guantanamo three years later.

The October 2002 bombings on the tourist island of Bali killed 202 people, including 88 Australians, and left a deep scar in Indonesia. The August 2003 attack on the JW Marriott Hotel in Jakarta killed 12 and wounded about 150.

In December, Indonesian police arrested a man believed to be the military leader of Jemaah Islamiyah network.

The most prominent Guantanamo case, involving five men charged in the September 11, 2001, terrorist attacks, has been stuck in the pre-trial phase since their arraignment in May 2012. No date for the death penalty trial has been set.

The US holds 40 men at Guantanamo. President Barack Obama sought to close the detention centre, move the prisoners to facilities inside the United States and try them in civilian court, but was blocked by Congress.

Biden favours closing the centre but has not yet disclosed his plans for the facility.

Australian Associated Press