A United States military judge has ruled that plea agreements reached with the alleged plotters of the September 11, 2001, attacks are valid, reversing an order by the country’s defence minister.

The order by the judge, Air Force Colonel Matthew McCall, means the three accused men may eventually be sentenced to life in prison instead of death as part of the deal reached earlier, The New York Times and The Associated Press news agency reported on Wednesday.

Defense Secretary Lloyd Austin rescinded the three separate pretrial agreements on August 2, two days after a senior Pentagon official signed them.

But the military judge at Guantanamo Bay in Cuba ordered that Khalid Sheikh Mohammed, the alleged mastermind, and two accused accomplices, Walid bin Attash and Mustafa al-Hawsawi, can appear before his court to enter pleas. He is reportedly yet to set a timetable.

The judge argued that Austin had the authority to exert supervision over the process when it was ongoing, but did not have the legal authority to rescind the plea deals as the defence minister.

The Pentagon was reviewing the judge’s decision and had no further comment, said its spokesman Major-General Pat Ryder. Prosecutors have also not commented on the ruling, which has not yet been publicly announced.

Mohammed and four others were charged in 2012 with conspiring in the attacks that killed nearly 3,000 people, but the cases have for years been mired in litigation over the torture of the defendants by the Central Intelligence Agency (CIA).

Pretrial hearings were scheduled at Guantanamo Bay in the case for another defendant, Ammar al-Baluchi, who has not reached a plea deal. The fifth defendant, Ramzi bin al-Shibh, was last September found incompetent to stand trial or reach a plea deal.

A forensic psychiatrist is reportedly expected to testify on Thursday on whether the defendants made their 2007 confessions under torture or voluntarily, after spending years in secret CIA prisons.

The cases are still expected to take a long time before reaching the finish line even if verdicts and sentences are reached. A US court of appeals would then likely have to hear many of the issues surrounding the cases – including the destruction of videos of interrogations by the CIA.

Mohammed was regarded as one of al-Qaeda chief Osama bin Laden’s most trusted men before he was captured in a covert operation in Pakistan in March 2003. He spent three years in secret CIA prisons before arriving in Guantanamo in 2006.

Bin Attash, a Saudi of Yemeni origin, allegedly trained two of the hijackers who carried out the attacks. He was captured with Mohammed in 2003 and was also held in a network of secret CIA prisons.

Al-Hawsawi is suspected of managing the finances for the 9/11 attacks. He was arrested in Pakistan on March 1, 2003, and was also held in secret prisons before being transferred to Guantanamo in 2006.