US prosecutors have reached a deal with 9/11 mastermind Khalid Sheikh Mohammed, the Pentagon said Wednesday, reportedly involving a guilty plea in exchange for avoiding a death penalty trial.

The agreements with Mohammed and two other accused moves their long-running cases toward resolution. These have been bogged down in pre-trial maneuverings for years while the defendants remained held at the Guantanamo Bay military base in Cuba.

A Pentagon statement said no details of the deal would be immediately made public at this time, but the New York Times reported that Mohammed, Walid bin Attash and Mustafa al-Hawsawi had agreed to plead guilty to conspiracy in exchange for a life sentence instead of a trial after they could get the death penalty.

Such a proposal was detailed by prosecutors in a letter last year but divided the families of the nearly 3,000 people killed in the September 11, 2001 attacks, with some still wanting the defendants to face the ultimate penalty.

Much of the legal jousting surrounding the men's cases has focused on whether they could be tried fairly after having undergone methodical torture at the hands of the CIA in the years after 9/11 - a thorny question that the plea deals help avoid.

This undated FBI file image shows Khalid Shaikh Mohammed, as he appeared on the FBI's Most Wanted Terrorists website. Photo: AFP

Mohammed was regarded as one of Al-Qaeda chief Osama bin Laden's most trusted and intelligent lieutenants before his March 2003 capture in Pakistan. He then spent three years in secret CIA prisons before arriving in Guantanamo in 2006.

The trained engineer - who has said he masterminded the 9/11 attacks "from A to Z" - was involved in a string of major plots against the United States, where he had attended university.

In addition to planning the operation to bring down the Twin Towers, Mohammed claims to have personally beheaded US journalist Daniel Pearl in 2002 with his "blessed right hand," and to have helped in the 1993 World Trade Center bombing that killed six people.

'War on Terror' prison

Bin Attash, a Saudi of Yemeni origin, allegedly trained two of the hijackers who carried out the September 11 attacks, and his US interrogators also said he confessed to buying the explosives and recruiting members of the team that killed 17 sailors in an attack on the USS Cole.

He took refuge in neighbouring Pakistan after the US invasion of Afghanistan in 2001 and was captured there in 2003, and was then held in a network of secret CIA prisons.

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.

The United States used Guantanamo, an isolated naval base, to hold militants captured during the "War on Terror" that followed the September 11 attacks in a bid to keep the defendants from claiming rights under US law.

The facility held 800 prisoners at its peak, but they have since slowly been repatriated to other countries. President Joe Biden pledged before his election to try and shut down Guantanamo, but it remains open.

In another 9/11-related case, the Justice Department denied a request by Zacarias Moussaoui, the so-called "20th hijacker," to serve the remainder of his life sentence in France.

In a hand-written letter to District Judge Leonie Brinkema obtained by the website Legal Insurrection, Moussaoui - the only person convicted in the United States in connection with the September 11 attacks - expressed fears he would be executed if Donald Trump regains the presidency in November.

A Justice Department spokeswoman said the department does not discuss prisoner transfer requests but noted that Moussaoui is "serving a life sentence following conviction for terrorism offences."

"The Department of Justice plans to enforce this life sentence in US custody," the spokeswoman added.