IMPEACH BUSH

WASHINGTON, Sept. 23 — The 21-year-old Jordanian immigrant was in shackles when he was brought into the courtroom of Judge Michael B. Mukasey in Federal District Court in Manhattan.

It was Oct. 2, 2001, and the prisoner, Osama Awadallah, then a college student in San Diego with no criminal record, was one of dozens of Arab men detained around the country in the days after the Sept. 11 attacks as potential witnesses in the terrorism investigation.

Before the hearing, Mr. Awadallah told his lawyer that he had been beaten in the federal detention center in Manhattan, producing bruises that were hidden beneath his orange prison jumpsuit. But when his lawyer told this to Judge Mukasey, the judge seemed little concerned.

"As far as the claim that he was beaten, I will tell you that he looks fine to me," said Judge Mukasey, who was nominated by President Bush last week to be his third attorney general and is now facing Senate confirmation hearings. "You want to have him examined, you can make an application. If you want to file a lawsuit, you can file a civil lawsuit."

Even though Mr. Awadallah was not charged at the time with any crime and had friends and family in San Diego who would vouch that he had no terrorist ties, Judge Mukasey ordered that he be held indefinitely, a ruling he made in the cases of several other so-called material witnesses in the Sept. 11 investigations. A prison medical examination later identified the bruises across his body.

Judge Mukasey's comments at the 2001 hearing were revealed in a once-secret 16-page transcript provided to The New York Times by a lawyer for Mr. Awadallah.

Although Mr. Mukasey is otherwise widely admired by prosecutors and defense lawyers alike in New York, his handling of the cases of Mr. Awadallah and other material witnesses taken into custody in terrorism investigations after Sept. 11 produced some rare, sharp criticism of his performance on the bench and raised concern among civil liberties groups. Senate Democrats have suggested they will focus on the issue when Mr. Mukasey is questioned at his confirmation hearings.

The White House has declined to answer detailed questions about Mr. Mukasey's record pending the Senate hearings. But the retired judge appeared to defend himself in an opinion article that was published in The Wall Street Journal last month in which he rebuffed criticism of the treatment of material witnesses after Sept. 11, saying their due process was protected.

"Each individual so arrested was brought immediately before a federal judge where he was assigned counsel, had a bail hearing and was permitted to challenge the basis for his detention, just as a criminal defendant would be," he wrote. The article made no reference to Mr. Awadallah's detention.

Critics say a 1984 material witness law was abused by the Justice Department, and by Judge Mukasey and his judicial colleagues, to hold terrorist suspects indefinitely after Sept. 11 without having to accuse them of a crime and afford them the rights of a criminal defendant.

The roundup of men like Mr. Awadallah under the material witness law in September and October 2001 was an early effort by the Bush administration to rewrite or reinterpret laws on the detention, interrogation and surveillance of people suspected of terrorist ties after the Sept. 11 attacks — a campaign that is now the subject of furious debate between the White House and the Democratic leaders of Congress.

Critics say the material witness cases before Judge Mukasey after Sept. 11 offer insight into his performance and temperament at a time of duress. The cases came before him at a time when New York was still in turmoil, with the courthouse in Lower Manhattan, only blocks from the rubble of the World Trade Center, partly shut down and operating under extraordinarily tight security.

Democrats on the Senate Judiciary Committee have said they will try to review cases like Mr. Awadallah's in detail before Mr. Mukasey, who retired last year after 18 years on the court, appears before them.

Senator Charles E. Schumer, the New York Democrat who encouraged Mr. Bush to consider Mr. Mukasey for the Justice Department job, said that he was aware of the concerns over the nominee's record on material witnesses cases, and that they would be studied by the committee. "There will certainly be those questions for him," Mr. Schumer said.

Congressional aides said that while the committee's chairman, Senator Patrick J. Leahy, Democrat of Vermont, thought it was too early to discuss specific questions that would be put to Mr. Mukasey, the senator has long been concerned about the possible abuse of the federal material witness statute in the indefinite detention of terrorist suspects.

The records of most material witnesses cases are sealed, so there is no way to determine whether Judge Mukasey's tone in the October 2001 hearing for Mr. Awadallah reflects his handling of other witnesses picked up after Sept. 11.

Some of Mr. Awadallah's records became public because he, unlike most of other material witnesses, was eventually charged with a crime. His odyssey in the federal court system ended last November, more than five years after his initial detention, when he was acquitted on charges that he lied to a grand jury when he denied that he knew one of the Sept. 11 hijackers.

After his acquittal, Mr. Awadallah returned home to California. As he awaited trial last year, he continued his studies and graduated with honors last year from San Diego State University.

Prominent defense lawyers and legal scholars have said that Judge Mukasey and other federal judges were too quick to accept the administration's reasoning after Sept. 11 that young Arab men should be held as "material witnesses" in terrorism investigations.

It was a ruse, the lawyers say, for the government to detain them, often for months at a time, without any need to cite evidence of possible wrongdoing.

Randy Hamud, the San Diego lawyer who represented Mr. Awadallah in the courtroom on that first hearing in October 2001, said he was startled by how "injudicious and malicious" Judge Mukasey had been toward his client.

He said Judge Mukasey seemed not to care that Mr. Awadallah and other witnesses had been whisked away to New York from San Diego without any notice to the lawyers and were denied the right to contact lawyers for hours after their arrival in New York.

"I wasn't aware that they were in New York until approximately 8:30 yesterday morning," Mr. Hamud told the judge at the Oct. 2 hearing, according to the transcript. Mr. Hamud said he had been required to fly overnight to New York from California to attend the early morning hearing.

"You are now aware of it," the judge replied without elaboration.

When Mr. Hamud asked Judge Mukasey why he was not admonishing prosecutors for blocking his contact with Mr. Awadallah, the judge replied: "Your question is ridiculous. The government isn't interfering with the attorney-client privilege."

The lawyer continued, "It is, Your Honor."

The judge replied, "Oh, please."

Mr. Hamud said he was also taken aback at the hearing when Judge Mukasey sided with prosecutors and refused to allow a prominent Arab-American criminal defense lawyer, Abdeen M. Jabara, to help defend Mr. Awadallah.

Prosecutors argued that Mr. Jabara had a conflict of interest because he defended Sheik Omar Abdel Rahman, the blind Egyptian cleric convicted in 1995 in a terrorist plot to blow up New York City landmarks. Judge Mukasey was the judge in that trial.

The transcript shows that Mr. Hamud, who had no background in criminal law, told the judge that he needed the help of an experienced New York criminal defense lawyer like Mr. Jabara.

"I am obviously a practitioner from Southern California," he said. "I am not familiar with the nuances of the Southern District." It was a reference to the Southern District of New York, the judicial region that includes the Manhattan courthouse.

Judge Mukasey replied, "Which nuances are you not familiar with?"

Mr. Hamud said, "Mr. Jabara has not had a chance to let me know those yet."

Judge Mukasey replied: "I got news for you. Mr. Jabara is not terribly familiar with the nuances either." He said that Mr. Jabara "was before me in a case that arguably has some relationship to this." He did not detail what that relationship might be.

In the years since the Sept. 11 attacks, federal law enforcement agencies have found no clear relationship between Sheik Abdel Rahman's followers and the 9/11 plot. Mr. Jabara did not return phone calls to his law office.

The Justice Department's widespread use of the 1984 federal material-witness law to detain dozens of young Arab men after the Sept. 11 attacks has been widely criticized by legal scholars as an abuse of the law, which was intended to prevent witnesses in criminal cases from fleeing before they could testify.

In a report in 2005, Amnesty International and Human Rights Watch said they had found evidence of at least 70 cases in which men living in the United States, all Muslims except one, had been "thrust into a Kafkaesque world of indefinite detention without charges" because they had been labeled material witnesses.

Jesse Berman, a New York lawyer who joined Mr. Awadallah's defense team after the Oct. 2 hearing and provided The Times with the transcript, said that there was no excuse for Judge Mukasey's performance at the hearing, even in the chaotic weeks after 9/11, when there was fear of another terrorist attack.

"It was a hard time, but it was a hard time for the material witnesses, too," he said. "Mukasey was not objective. He's an advocate of the prosecutorial side of things." But Judge Mukasey's handling of the cases is likely to have support among some in the Bush administration. Viet D. Dinh, a former assistant attorney general in the Bush Justice Department and now a law professor at Georgetown University, said Judge Mukasey was following a "fairly straightforward application of the material witness statute" in the post-9/11 cases.

What was different, Professor Dinh said, was how many more of the cases there were after the terror attacks.

"It would be like criticizing a judge for applying the murder laws because too many prosecutors have been bringing murder cases," he said. "It's certainly not a fair criticism."