The US Attorney General, Ms Janet Reno, has refused to apologise to Dr Wen Ho Lee, the Los Alamos nuclear scientist who has been released from nine months of solitary confinement after the government dropped 58 charges of breaching national security.
But President Clinton has said that it is hard to see the justice for holding Dr Lee in custody for that time in view of what has happened.
Dr Lee pleaded guilty to one count of mishandling nuclear weapons data and was sentenced to the 278 days he had served in prison while awaiting trial. He has also agreed to be questioned by the FBI on missing tapes of data that he downloaded from his computer, which the prosecution had claimed were the "crown jewels" of the US nuclear weapons programme.
Mr Lee has said he destroyed the seven missing tapes and the prosecution now admits that it misled the judge over the importance of the data after Dr Lee's arrest late last year.
At the time there was a widespread scare that Dr Lee and other Chinese-American scientists might have passed secrets to China which helped it to develop its nuclear weapons. The Republican-controlled Congress had earlier held hearings about alleged Chinese espionage and interference in recent US elections.
Judge James Parker apologised to Mr Lee - a naturalised US citizen who was born in Taiwan - for having denied him bail at the insistence of the prosecution. "Dr Lee, I tell you with great sadness that I was led astray by the executive branch of government," the judge said.
The judge said that "top decision-makers" in the government "did not embarrass me alone but they embarrassed this entire nation and everyone who is a citizen of it".
Mr Lee was given an enthusiastic welcome by about 200 of his neighbours and co-workers in Los Alamos who sang "For He's a Jolly Good Fellow" when he returned home. The prosecution had insisted that he be held in solitary confinement for the past nine months and that he be shackled when he took exercise.
But Ms Reno was unrepentant yesterday when she said she was "comfortable" with her department's handling of Dr Lee's case. She wished that he had early on provided investigators with information about the missing computer tapes. He now "needs to look to himself" rather than expect an apology from the US government, she said at her weekly press conference.
The US attorney in New Mexico, Mr George Stamboulidis, objected to Judge Parker's criticism, saying that the prosecutors were right to insist that Dr Lee be held in solitary confinement.
If during the interrogation of Dr Lee the FBI believes that he is lying and can persuade Judge Parker of that, he could be prosecuted on all 59 charges in the original indictment and also for perjury and obstruction of justice.