Legal experts have criticized the U.S. decision, and The Associated Press filed a letter of protest, arguing that it would be "an unconstitutional mistake to close the proceedings in their entirety."
The transcripts refer to a claim by Mohammed that he was tortured by the CIA, although he said he was not under duress at Guantanamo when he confessed to his role in the attacks. The CIA has said its interrogation practices are legal, and it does not use torture.
Kenneth Roth, executive director of Human Rights Watch, questioned the legality of the closed-door sessions and whether the confession was actually the result of torture.
"We won't know that unless there is an independent hearing," he said. "We need to know if this purported confession would be enough to convict him at a fair trial or would it have to be suppressed as the fruit of torture?"
In listing the 28 attacks he planned and another three he supported, Mohammed said he tried to kill international leaders including Pope John Paul II, President Bill Clinton and Pakistani President Pervez Musharraf.
He said he planned the 2002 bombing of a Kenya beach resort frequented by Israelis and the failed missile attack on an Israeli passenger jet after it took off from Mombasa, Kenya.
He also said he was responsible for the bombing of a nightclub in Bali, Indonesia. In 2002, 202 were killed when two nightclubs there were bombed.
Other plots he said he was responsible for included planned attacks against the Sears Tower in Chicago, the Empire State Building and New York Stock Exchange in New York City, the Panama Canal, and Big Ben and Heathrow Airport in London - none of which happened.
The Pentagon also released transcripts of the hearings of Abu Faraj al-Libi and Ramzi Binalshibh. Both refused to attended the hearings, although al-Libi submitted a statement claiming that the hearings are unfair and that he will not attend unless they are corrected.
"The detainee is in a lose-lose situation," he said.
Al-Libi, whose surname means he is a Libyan, reportedly masterminded two bombings 11 days apart in Pakistan in December 2003 that targeted Musharraf for his support of the U.S.-led war on terror.
Binalshibh, a Yemeni, is suspected of helping Mohammed with the Sept. 11 attack plan on New York City and Washington and is also linked to a foiled plot to crash aircraft into London's Heathrow Airport. His hearing was conducted in his absence.
Associated Press writers Lolita C. Baldor and Matthew Lee contributed to this report.
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