WASHINGTON — The Pentagon has charged six detainees at Guantanamo Bay with murder and war crimes in connection with the September 11, 2001 attacks, it was announced today. Officials said they’ll seek the death penalty in what would be the first trials under the terrorism-era military tribunal system.

“These charges allege a long term, highly sophisticated, organized plan by Al Qaeda to attack the United States of America,” the legal adviser to the tribunal system, Brigadier General Thomas Hartmann, told reporters. He added that the charges have been sworn “against six individuals alleged to be responsible for the planning and execution of the attacks” which killed nearly 3,000 people.

General Hartmann said the six include the suspected mastermind of the attacks in which hijacked planes were flown into buildings in New York and Washington, Khalid Sheikh Mohammed. Another hijacked plane crashed in the fields of western Pennsylvania.

The military will recommend that the six men be tried together before a military tribunal. The cases may be clouded because of recent disclosures that Mohammmed was subject to an interrogation technique known as waterboarding — which critics call torture.

Asked what impact that will have on the case, General Hartmann said it will be up to the military judge to determine what evidence is allowed.

Prosecutors have been working for years to assemble the case against suspects in the attacks that prompted the Bush administration to launch its global war on terror.

The other five men being charged are: the man officials have labeled the 20th hijacker, Mohammed al-Qahtani; a man to have been the main intermediary between the hijackers and leaders of Al Qaeda, Ramzi Binalshibh; a man known as Ammar al-Baluchi, a nephew of Khalid Sheikh Mohammed, who has been identified as Mohammed’s lieutenant for the 2001 operation, Ali Abd al-Aziz Ali; al-Baluchi’s assistant, Mustafa Ahmad al-Hawsawi; and a detainee known as Khallad, who investigators say selected and trained some of the hijackers, Waleed bin Attash.

A White House spokeswoman, Dana Perino, said that President Bush had no role in the decision to seek the death penalty.

“Obviously 9-11 was a defining moment in our history,” she said, “and a defining moment in the global war on terror. And this judicial process is the next step in that story. The president is sure that the military is going to follow through in a way that the Congress said they should.”

The men would be tried in the military tribunal system that was set up by the administration shortly after the start of the counterterror war. Original rules allowed the military to exclude the defendant from his own trial, permitted statements made under torture, and forbade appeal to an independent court; but the U.S. Supreme Court struck down the system in 2006 and a revised plan set up after Congress enacted a new law has included some additional rights.

Defense lawyers still criticize the system for its secrecy.

General Hartmann said today that the defendants will get the same rights as American soldiers tried under the military justice system including the right to remain silent, call witnesses, and know the evidence against him. Appeals can go all the way to the U.S. Supreme Court.

He called the charges sworn today “only allegations” and said the accused will remain innocent until proven guilty.

The decision to seek the death penalty also is likely to draw criticism from within the international community. A number of countries, including American allies, have said they would object to the use of capital punishment for their nationals held at Guantanamo.

The military tribunal system requires that a panel of 12 unanimously find the defendant guilty for capital punishment cases, General Hartmann said.

Officials plan to hold the trial in a specially constructed court at Guantanamo that will allow lawyers, journalists, and some others to be present, but leave relatives of September 11, 2001 victims and others to watch the trial through closed-circuit broadcasts.

Mohammed was among 15 so-called “high-value detainees” who were held at length by the CIA in secret overseas prisons — some subject to what critics call torture — before being handed over to the military in 2006.

Last week, for the first time, the Bush administration acknowledged that Mohammed was among three suspects who were waterboarded. The director of the CIA, Michael Hayden, said that waterboarding was used, in part, because of widespread belief among American intelligence officials that more catastrophic attacks were imminent.

Waterboarding involves strapping a person down and pouring water over the suspect’s cloth-covered face to create the sensation of drowning.

In Guantanamo Bay hearings that have been criticized as unfair, Mohammed confessed to the September 11, 2001 attacks and a chilling string of other terror plots last March.

“I was responsible for the 9/11 operation from A to Z,” Mohammed said in a statement read during the session, according to hearing transcripts later released by the Pentagon.

Under the system, the charges are forwarded to the convening authority for military commissions, Susan Crawford. She can refer some or all of them for trial.

And it could be months or longer before trials begin for the six defendants. With the appeals process, it would likely be some time after any convictions before executions would be possible.