A US military appeals court has ruled that plea deals related to the man accused of masterminding the September 11, 2001, attacks and two accomplices can proceed after Defense Secretary Lloyd Austin had earlier moved to invalidate the agreements.

In August, Austin rescinded plea deals that the Pentagon had entered into with the trio, including Khalid Sheikh Mohammed.

In November, a US military judge ruled that Austin acted too late in revoking the plea deals and that they were still valid. The order late on Monday by the US military appeals court upheld that ruling.

It has previously said Austin was surprised by the plea deals and that the secretary was not consulted because that process is independent.

Under the deals, it is possible that the three men could plead guilty to the attacks and, in exchange, not face the death penalty.

Austin now has the option of taking his effort to throw out the plea deals to the US Court of Appeals for the District of Columbia Circuit.

Khalid Sheikh Mohammed is the most widely known inmate at the US detention facility known as Guantanamo Bay on the coast of Cuba. It was set up in 2002 by then-US President George W. Bush to detain foreign suspects following the September 11 attacks on the United States.

He is accused of masterminding the plot to fly hijacked commercial passenger aircraft into the World Trade Center in New York City and into the Pentagon. The 9/11 attacks, as they are known, killed nearly 3,000 people.

Notorious Guantanamo

Human rights experts, including at the United Nations, have condemned torture at Guantanamo Bay and elsewhere during the so-called war on terror and demanded an apology from Washington.

Former president Barack Obama acknowledged in 2014 that the US had engaged in torture and said it was "contrary to our values."

Separately on Monday, the Pentagon said that Ridah Bin Saleh Al-Yazidi, one of the longest-held detainees at Guantanamo Bay, was repatriated from the detention facility to his home country of Tunisia. He was held without charge for over 20 years.

The Pentagon said 26 detainees remained at the facility, of whom 14 are eligible for transfer.

Guantanamo became a symbol of US abuses and the centre of worldwide controversy over the violations of detainees' rights.

President Joe Biden hoped to close the facility, but it remains open as President-elect Donald Trump is set to take office.