Some families of the victims had condemned the deal for cutting off any possibility of full trials and possible death penalties.
Republicans had been quick to fault the Biden administration for the deal, although the White House said after it was announced it had no knowledge of it.
Tom Cotton, a Republican senator in Arkansas and a member of the Armed Services Committee, condemned the plea deal on social media as “disgraceful”. He said he had introduced legislation that would mandate the defendants face trial and the possibility of the death penalty.
Bogged-down
The US military commission overseeing the cases of five 9/11 defendants has been bogged-down in pre-trial hearings and other preliminary court action since 2008, while the accused are still held at the US Guantanamo Bay military base in Cuba.
The prospect of full trials and verdicts is still uncertain, in part because of the inadmissibility of evidence linked to torture that the defendants underwent in CIA custody.
Lawyers for the two sides have been exploring a negotiated resolution to the case for about a year and a half.
Mr Mohammed – whom the US describes as the main plotter of the attack that crashed hijacked passenger planes into the World Trade Center, the Pentagon and a Pennsylvania field – and the other two defendants had been expected to enter their pleas under the deal as soon as next week.
Legally fraught
J Wells Dixon, a staff attorney at the Center for Constitutional Rights has represented the defendants at Guantanamo, as well as other detainees there who have been cleared of any wrongdoing. He had welcomed the plea bargains as the only feasible way to resolve the long-stalled and legally fraught cases.
On Friday, Mr Dixon accused Mr Austin of “bowing to political pressure and pushing some victim family members over an emotional cliff” by rescinding the plea deals.
Joe Biden blocked an earlier proposed plea bargain in the case last year, when he refused to offer presidential guarantees that the men would be spared solitary confinement and provided trauma care for the torture they underwent.
A fourth 9/11 defendant at Guantanamo was earlier still negotiating a possible plea agreement.
The military commission last year ruled a fifth defendant mentally unfit to stand trial. A military medical panel cited post-traumatic stress disorder and psychosis, and linked it to torture and solitary confinement in four years in CIA custody before transfer to Guantanamo.