Twice in the past four years, a top Justice Department lawyer warned the presiding judge of a secret surveillance court that information overheard in President Bush's eavesdropping program may have been improperly used to obtain wiretap warrants in the court, according to two sources with knowledge of those events.

The revelations infuriated U.S. District Judge Colleen Kollar-Kotelly -- who, like her predecessor, Royce C. Lamberth, had expressed serious doubts about whether the warrantless monitoring of phone calls and e-mails ordered by Bush was legal. Both judges had insisted that no information obtained this way be used to gain warrants from their court, according to government sources, and both had been assured by administration officials it would never happen.

The two heads of the Foreign Intelligence Surveillance Court were the only judges in the country briefed by the administration on Bush's program. The president's secret order, issued sometime after the Sept. 11, 2001, attacks, allows the National Security Agency to monitor telephone calls and e-mails between people in the United States and contacts overseas.

James A. Baker, the counsel for intelligence policy in the Justice Department's Office of Intelligence Policy and Review, discovered in 2004 that the government's failure to share information about its spying program had rendered useless a federal screening system that the judges had insisted upon to shield the court from tainted information. He alerted Kollar-Kotelly, who complained to Justice, prompting a temporary suspension of the NSA spying program, the sources said.

Yet another problem in a 2005 warrant application prompted Kollar-Kotelly to issue a stern order to government lawyers to create a better firewall or face more difficulty obtaining warrants.

The two judges' discomfort with the NSA spying program was previously known. But this new account reveals the depth of their doubts about its legality and their behind-the-scenes efforts to protect the court from what they considered potentially tainted evidence. The new accounts also show the degree to which Baker, a top intelligence expert at Justice, shared their reservations and aided the judges.

Both judges expressed concern to senior officials that the president's program, if ever made public and challenged in court, ran a significant risk of being declared unconstitutional, according to sources familiar with their actions. Yet the judges believed they did not have the authority to rule on the president's power to order the eavesdropping, government sources said, and focused instead on protecting the integrity of the FISA process.

It was an odd position for the presiding judges of the FISA court, the secret panel created in 1978 in response to a public outcry over warrantless domestic spying by J. Edgar Hoover's FBI. The court's appointees, chosen by then-Chief Justice William H. Rehnquist, were generally veteran jurists with a pro-government bent, and their classified work is considered a powerful tool for catching spies and terrorists.

The FISA court secretly grants warrants for wiretaps, telephone record traces and physical searches to the Justice Department, whose lawyers must show they have probable cause to believe that a person in the United States is the agent of a foreign power or government. Between 1979 and 2004, it approved 18,748 warrants and rejected five.

Lamberth, the presiding judge at the time of the Sept. 11 attacks, and Kollar-Kotelly, who took over in May 2002, have repeatedly declined to comment on the program or their efforts to protect the FISA court. A Justice Department spokesman also declined to comment.

Both presiding judges agreed not to disclose the secret program to the 10 other FISA judges, who routinely handled some of the government's most highly classified secrets.

So early in 2002, the wary court and government lawyers developed a compromise. Any case in which the government listened to someone's calls without a warrant, and later developed information to seek a FISA warrant for that same suspect, was to be carefully "tagged" as having involved some NSA information. Generally, there were fewer than 10 cases each year, the sources said.

According to government officials familiar with the program, the presiding FISA judges insisted that information obtained through NSA surveillance not form the basis for obtaining a warrant and that, instead, independently gathered information provide the justification for FISA monitoring in such cases. They also insisted that these cases be presented only to the presiding judge.

Lamberth and Kollar-Kotelly derived significant comfort from the trust they had in Baker, the government's liaison to the FISA court. He was a stickler-for-rules career lawyer steeped in foreign intelligence law, and had served as deputy director of the office before becoming the chief in 2001.

Baker also had privately expressed hesitation to his bosses about whether the domestic spying program conflicted with the FISA law, a government official said. Justice higher-ups viewed him as suspect, but they also recognized that he had the judges' confidence and kept him in the pivotal position of obtaining warrants to spy on possible terrorists.

In 2004, Baker warned Kollar-Kotelly he had a problem with the tagging system. He had concluded that the NSA was not providing him with a complete and updated list of the people it had monitored, so Justice could not definitively know -- and could not alert the court -- if it was seeking FISA warrants for people already spied on, government officials said.

Kollar-Kotelly complained to then-Attorney General John D. Ashcroft, and her concerns led to a temporary suspension of the program. The judge required that high-level Justice officials certify the information was complete -- or face possible perjury charges.

In 2005, Baker learned that at least one government application for a FISA warrant probably contained NSA information that was not made clear to the judges, the government officials said. Some administration officials explained to Kollar-Kotelly that a low-level Defense Department employee unfamiliar with court disclosure procedures had made a mistake.

Kollar-Kotelly asked Defense Secretary Donald H. Rumsfeld to ensure that wouldn't happen again, government officials said.

Baker declined to comment through an office assistant, who referred questions about his FISA work to a Justice Department spokesman. Pentagon spokeswoman Cynthia Smith also declined to comment and referred questions to Justice officials. Justice spokesman Brian Roehrkasse said the department could not discuss its work with the FISA court.

"The department always strives to meet the highest ethical and professional standards in its appearances before any court, including the FISA court," Roehrkasse said. "This is especially true when department attorneys appear before a court on an ex parte basis, as is the case in the FISA court."

Shortly after the warrantless eavesdropping program began, then-NSA Director Michael V. Hayden and Ashcroft made clear in private meetings that the president wanted to detect possible terrorist activity before another attack. They also made clear that, in such a broad hunt for suspicious patterns and activities, the government could never meet the FISA court's probable-cause requirement, government officials said.

So it confused the FISA court judges when, in their recent public defense of the program, Hayden and Attorney General Alberto R. Gonzales insisted that NSA analysts do not listen to calls unless they have a reasonable belief that someone with a known link to terrorism is on one end of the call. At a hearing Monday, Gonzales told the Senate Judiciary Committee that the "reasonable belief" standard is merely the "probable cause" standard by another name.

Several FISA judges said they also remain puzzled by Bush's assertion that the court was not "agile" or "nimble" enough to help catch terrorists. The court had routinely approved emergency wiretaps 72 hours after they had begun, as FISA allows, and the court's actions in the days after the Sept. 11 attacks suggested that its judges were hardly unsympathetic to the needs of their nation at war.

On Sept. 12, Bush asked new FBI Director Robert S. Mueller III in a Cabinet meeting whether it was safe for commercial air traffic to resume, according to senior government officials. Mueller had to acknowledge he could not give a reliable assessment.

Mueller and Justice officials went to Lamberth, who agreed that day to expedited procedures to issue FISA warrants for eavesdropping, a government official said.

The requirement for detailed paperwork was greatly eased, allowing the NSA to begin eavesdropping the next day on anyone suspected of a link to al Qaeda, every person who had ever been a member or supporter of militant Islamic groups, and everyone ever linked to a terrorist watch list in the United States or abroad, the official said.

In March 2002, the FBI and Pakistani police arrested Abu Zubaida, then the third-ranking al Qaeda operative, in Pakistan. When agents found Zubaida's laptop computer, a senior law enforcement source said, they discovered that the vast majority of people he had been communicating with were being monitored under FISA warrants or international spying efforts.

"Finally, we got some comfort" that surveillance efforts were working, said a government official familiar with Zubaida's arrest.

Commentary:
Where is the Supreme Court in this mess. If only two FISA judges and few members of congress were aware Bush was breaking the law shouldn't someone have done something, like take it to the Supreme Court?