In a motion filed Wednesday, Richard Reid said he would plead guilty to attempted murder and all other charges against him, but asked the court to remove accusations concerning al Qaeda.
"The Justice Department stands by each and every allegation in the indictment. We are prepared to substantiate all of the charges," Attorney General John Ashcroft said in a statement.
Ashcroft said Reid acted on his own in filing the motion and has no plea agreement with the government. Reid earlier lost a bid to remove the same language from the indictment against him.
U.S. District Court Judge William G. Young scheduled a change of plea hearing for Friday.
Attorney Owen Walker said Reid wanted to avoid the publicity of a trial and the negative impact it would have on his family.
Reid, a 29-year-old British citizen, faces up to life in prison if convicted of the most serious charges. His attorney said Reid "has no disagreement with the facts" asserted in the charges.
Reid's motion does not say a guilty plea is contingent upon the al Qaeda references being stricken. Walker declined comment on the issue.
In their motion, Reid's defense lawyers said prosecutors had told them they did not plan to introduce evidence of an al Qaeda link during Reid's trial.
But federal prosecutors denied that and filed a pleading that opposed removal of any language from the indictment.
"Clearly, there's a misunderstanding on the part of Mr. Reid's attorneys," U.S. Attorney Michael Sullivan said.
Reid is accused of attempting to kill the 197 passengers and crew members aboard American Airlines Flight 63 from Paris to Miami on Dec. 22. He was overpowered by flight attendants and passengers, and the flight was diverted to Boston. Trial was set for Nov. 4.
Authorities said each shoe contained a plastic explosive often used by terrorists. They said the homemade bombs could easily have ripped a hole in the plane.
The indictment said Reid "received training from al Qaeda in Afghanistan," but it provided no other details about Reid's alleged ties to the terrorist network.
The FBI has said it believes Reid had help making the bomb from "an al Qaeda bomb maker," and have cited unidentified human hair and a palm print found on the explosives.
Reid insisted to FBI investigators he acted alone.
In statements to law enforcement after his arrest, Reid said he acted because of the U.S. military campaign in Afghanistan and that he hoped his planned attack would cause Americans to stop traveling, leading to a downturn in the economy, prosecutors said.
Reid also told the FBI he was driven by anger over the treatment of Muslims in Israel, according to transcripts of the interrogations. He said he traveled in 2001 to Jerusalem's Al Aqsa Mosque, and was angered to see "Jews with guns" inside.
Asked why he didn't choose to attack Israel, Reid told investigators: "America is the problem, without America there would be no Israel." He also said he was worried Palestinian groups would be too paranoid to trust him.
Reid converted to Islam while in prison for petty crimes. He later worshipped at the same London mosque as Zacarias Moussaoui, who has been charged with conspiracy in the Sept. 11, 2001, attacks.