WASHINGTON — Bush administration officials said Tuesday that they were confident that charges against six suspected members of Al Qaeda would survive expected defense contentions that the cases are based on unreliable statements obtained using harsh interrogation methods.

The officials confirmed that the Justice Department and the Pentagon, aware of probable legal challenges involving possible mistreatment of prisoners, began an extensive effort in late 2006 to rebuild the cases against the six men using what officials called “clean teams” of agents and military investigators.

By interviewing the prisoners again, and reassembling other evidence against them, the prosecutors could present evidence in court that would be harder for defense lawyers to challenge. But some legal experts said that approach might not defuse defense arguments that the initial investigations were tainted.

The chief military prosecutor for detainees held at Guantánamo Bay in Cuba, Col. Lawrence J. Morris of the Army, declined to discuss the details of how prosecutors would deal with questions about the treatment of captured terrorism suspects. But, Colonel Morris added, “we will take very seriously our burden to present trustworthy evidence on which a panel can rely” in reaching a verdict.

Dozens of F.B.I. agents have spent hundreds of hours at the Guantánamo detention center interviewing potential witnesses and suspects. In effect, they recreated intelligence files, thus avoiding information that might be tainted because it was obtained during interrogations using harsh techniques. The legal tactic was described on Tuesday by The Washington Post.

The C.I.A. confirmed last week that one of the six defendants, Khalid Sheikh Mohammed, considered the chief plotter of the 2001 attacks, was subjected to the technique known as waterboarding, considered by many legal authorities to be torture, while in C.I.A. custody.

In addition to Mr. Mohammed, military prosecutors filed charges on Monday against Mohammed al-Qahtani, sometimes described as the “20th hijacker,” who was denied entry into the United States in August 2001; and four men who officials believe played a logistical role in the plot, Ramzi bin al-Shibh, Ali Abd al-Aziz Ali, Mustafa Ahmed al-Hawsawi and Walid bin Attash. The charges, for which prosecutors are seeking the death penalty, include conspiracy, murder, attacking civilians, terrorism and providing material support for terrorism.

The clean-team investigators, who had not been briefed on earlier interrogations by the C.I.A. using harsher tactics, adopted non-confrontational interview techniques. One government official said some of those charged this week spoke openly about their roles in the Sept. 11 plot.

The investigators applied many of the same standards in Guantánamo that are commonly used in criminal cases in the United States. But unlike suspects in criminal cases, the Guantánamo detainees were not allowed to have a lawyer present during the interviews.

Agents involved in the interviews were handpicked for their language and interview skills, law enforcement officials said. They spent many hours studying their assigned suspects and consulting with behavioral scientists before designing strategies to elicit the information they wanted.

While C.I.A. interrogations of the same suspects, sometimes using harsh physical pressure, were aimed largely at preventing more attacks, a government official said the clean-team interviews were intended to obtain information about past plots in order to build a prosecution.

Kenneth Wainstein, chief of the national security division at the Justice Department, said in a telephone interview that federal prosecutors assigned to the Guantánamo cases had been centrally involved in the investigation since 14 alleged senior Qaeda operatives were moved to Guantánamo in September 2006.

Mr. Wainstein said the investigators had been advised by “seasoned prosecutors who are very adept at building cases and anticipating the challenges down the road.”

But Samuel Issacharoff, a New York University law professor, questioned whether the repeat interrogations could eliminate the taint of previous harsh treatment.

“No amount of redoing the interrogation would clean that up,” Mr. Issacharoff said. “There’s no such thing as a do-over when you have an abuse of fundamental rights.”

Jameel Jaffer, an American Civil Liberties Union lawyer and co-author of a book on treatment of prisoners, said that the law setting up military commissions banned outright any evidence obtained by torture. The judge decides whether to admit information produced using coercive techniques short of torture, a provision that defense lawyers are likely to use aggressively, Mr. Jaffer said.

“Every time they try to introduce a piece of evidence, the defense lawyers are going to say, ‘This piece of evidence is unreliable’ ” because of coercion, Mr. Jaffer said.

William Glaberson and Mark Mazzetti contributed reporting.

Copyright 2008 The New York Times Company