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 going to trial.
Details of the deal have not been announced, but US news outlets say the men will plead guilty in exchange for the prosecution 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.
They were the deadliest assault on US soil since the 1941 Japanese attack on Pearl Harbour, Hawaii, where 2,400 people were killed.
The plea deal was first announced in a letter sent by prosecutors to the families of victims, according to The New York Times.
It said the plea before a military court could come as early as next week.
In its announcement, the US defence department said "the specific terms and conditions of the pretrial agreements are not available to the public at this time".
The men have been accused of a litany of charges, including attacking civilians, murder in violation of the laws of war, hijacking and terrorism.
Khalid Sheikh Mohammed 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 fourth plane crashed into a field in Pennsylvania after passengers fought back.
Mohammed, 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.
The trial has been delayed for so long partly because of fears that the so-called brutal interrogation techniques which critics say amounted to torture could have undermined the evidence against the detainees.
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 Mohammed.
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 new deal and had played no role in negotiations.
Jim Smith, whose wife died in the attacks, told the New York Post 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.
Republicans, too, were quick to attack the Biden administration for striking a deal with the accused.
Senate Minority Leader Mitch McConnell condemned the move as "a revolting abdication of the government's responsibility to defend America and provide justice".
"The only thing worse than negotiating with terrorists is negotiating with them after they are in custody," he said.
AzVision.az
More about: UnitedStates Pentagon NewYork 9/11attacks
