The sources tell CNN that Lee has agreed to cooperate with the Justice Department and will tell them what happened to a number of missing computer tapes which held classified information about nuclear weapons design.
The Associated Press reported that, according to two senior officials, Lee will be sentenced to time already served and immediately freed under the plea agreement.
The 60-year-old Taiwanese-born researcher, who worked for the Los Alamos National Laboratory in New Mexico, is charged with 59 counts of illegally copying what federal prosecutors called "the crown jewels" of U.S. nuclear weapons design. He never was charged with espionage.
Lee, who was fired last year and has been in solitary confinement in jail since December, had pleaded not guilty to all counts.
Trial was scheduled for November
A federal appeals court was scheduled on Monday to hear arguments on whether Lee would pose a danger to national security if he were freed on bail. He faced trial in November and could have received life imprisonment if found guilty.
The appeals court was scheduled to hear from prosecutors and defense attorneys on whether a trial judge in New Mexico acted properly in ordering Lee's release on $1 million bail.
U.S. District Judge James Parker, in Albuquerque, New Mexico, had said "it is no longer indisputable ... that the missing tapes contain crown jewel information about the nation's nuclear weapons program."
The judge also said he was concerned that an FBI agent admitted that some testimony he originally gave was incorrect.
Parker had ordered Lee's release and set out a 12-point list of "highly restrictive" conditions for Lee, limiting him to his house and back yard and subjecting his wife to searches by the FBI when she goes out or comes home.
But just minutes before Lee was scheduled to be set free on September 1, the 10th Circuit Court of Appeals in Denver issued an order stopping him from going home.
CNN Justice Correspondent Pierre Thomas and Reuters contributed to this report.
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