
The men have been accused of a litany of charges, including attacking civilians, murder in violation of the laws of war, hijacking and terrorism.
They are expected to formally submit their pleas in court as early as next week, the Times reported.
In September, the Biden administration reportedly rejected the terms of a plea deal with five men held at the US Navy base in Cuba, including Mohammad.
The men had reportedly sought a guarantee from the president that they would not be kept in solitary confinement and would have access to trauma treatment.
The White House National Security Council said that the president’s office was told on Wednesday of the deal and had played no role in the plea deal negotiations.
Khalid Sheikh Mohammad is widely considered the architect of the attack, in which hijackers seized passenger planes and crashed them into the World Trade Center in New York and the Pentagon outside of Washington.
A third plane crashed into a field in Pennsylvania after passengers fought back.
Mohammad, a US-educated engineer, was captured along with Hawsawi in Pakistan in March 2003.
Prosecutors argued that he brought his idea of hijacking and flying planes into US buildings to al-Qaeda leader Osama bin Laden, and later helped recruit and train some of the hijackers.
He was subjected to a number of “enhanced interrogation techniques”, including “waterboarding” – simulated drowning – at least 183 times before the practice was banned by the US government.
In his letter, Admiral Rugh wrote that the decision to accept the deal was “not reached lightly” and was in the “best path… to justice”.
However Jim Smith, whose wife died in the attacks, told the New York Post, external that families of victims had “waited 23 years to have our day in court to put on the record what these animals did to our loved ones”.
“They took that opportunity away from us,” he said, adding they should receive the “highest penalty” for their roles.
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