WASHINGTON -- U.S. authorities have long considered Mohammed al-Qahtani one of the most dangerous alleged terrorists in U.S. custody, a man who could have been the 20th hijacker in the Sept. 11, 2001, plot if he had not been denied entry into the country.

But yesterday, amid concerns about using information obtained during abusive military interrogations, a top Pentagon official removed Mr. Qahtani from the military commission case meant to bring justice to those behind the vast Sept. 11 conspiracy.

Susan Crawford, the appointed official who decides which cases will be heard in the largely untested commission process, dismissed the charges against Mr. Qahtani while affirming those against five other alleged terrorists to stand trial at the U.S. detention facility at Guantanamo Bay, Cuba.

Prosecutors reserve the right to charge Mr. Qahtani again, and the military says it can hold him without trial for the duration of the counterterrorism wars.

But his defense lawyers and officials familiar with the case say it is unlikely that Mr. Qahtani will face new charges because he was subjected to aggressive Defense Department interrogation techniques -- such as intimidation by dogs, hooding, nudity, long-term isolation and stress positions. Those techniques were later rescinded because of concerns about their legality.

In 2005, an official military investigation concluded that Mr. Qahtani's interrogation regimen amounted to abuse. Officials close to the case said Ms. Crawford's office was reluctant to sanction the charges against Mr. Qahtani because prosecutors had little evidence against him outside of his own coerced confessions -- a point that most certainly would have become a central issue at trial.

"Their case was only based on evidence derived from torture," said Army Lt. Col. Bryan Broyles, who represents Mr. Qahtani. "In six-plus years, the evidence comes down to what they beat out of him. The prosecution evidence was entirely unreliable and inadmissible."

Ms. Crawford has not commented publicly since taking over as the top official for military commissions, and a Pentagon spokesman yesterday said she has not explained her decision. Officials close to the case said the office's top legal adviser, Air Force Brig. Gen. Thomas Hartmann, concluded in an analysis that Mr. Qahtani's case was too weak to prosecute.

From the outset, Mr. Qahtani's case appeared to be an odd companion to the co-conspirator trial, as the other cases involve detainees -- such as alleged mastermind Khalid Sheik Mohammed -- held by the CIA, and they involve high-level allegations of conspiracy to commit the attacks, including financing, running al-Qaida training camps and helping the hijackers carry out the plot. Mr. Qahtani is alleged to be a field operative.

Human-rights organizations have been warning that harsh treatment of detainees would come back to haunt the U.S. government. Although some of the other five detainees were subjected to harsh interrogations by the CIA, the military organized a coordinated effort to re-interview them after they arrived at Guantanamo Bay in September 2006, using rapport-building methods. The results yielded incriminating evidence, officials said. But the same "clean teams" were not successful with Mr. Qahtani.

"Mr. Qahtani has never made a statement that was not extracted without torture," said Vincent Warren, executive director of the Center for Constitutional Rights, which also represents Mr. Qahtani.

The charges approved against the alleged co-conspirators detail 169 overt acts in support of the Sept. 11 attacks.