Khalid Sheikh Mohammed, Walid Muhammad Salih Mubarak Bin Attash and Mustafa Ahmed Adam al-Hawsawi have been held at the US Navy base at Guantanamo Bay, Cuba, for years without trial.
Details of the deal have not been released, but US news outlets say the men will plead guilty in exchange for prosecutors agreeing not to seek the death penalty.
Nearly 3,000 people in New York, Virginia and Pennsylvania were killed in the attacks, which sparked the “War on Terror” and the invasions of Afghanistan and Iraq.
It was the deadliest attack on American soil since the 1941 Japanese attack on Pearl Harbor, Hawaii, which killed 2,400 people.
The plea deal was first announced in a letter prosecutors sent to the victims’ families, according to the New York Times.
He said the appeal before a court-martial could be made as early as next week.
In its statement, the US Department of Defense said that “the specific terms and conditions of the pre-trial agreements are not publicly available at this time.”
The men have been charged with a range of charges including attack on civilians, murder in violation of the laws of war, hijacking and terrorism.
Khalid Sheikh Mohammed is widely believed to be the architect of the attack, in which hijackers hijacked passenger planes and crashed them into the World Trade Center in New York and the Pentagon outside Washington.
A fourth plane crashed in a field in Pennsylvania after passengers fought back.
Mohammed, a US-educated engineer, was arrested along with Hausawi in Pakistan in March 2003.
Prosecutors argued that he took 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 series of “enhanced interrogation techniques”, including waterboarding – simulated drowning – at least 183 times before the practice was banned by the US government.
The trial has been delayed for so long in part because of fears that the so-called brutal interrogation techniques, which critics say amounted to torture, could undermine the evidence against the detainees.
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