"This is the best way to protect our country, while upholding our deeply held values," the president said in a statement.
Obama had criticized the system established by President George W. Bush, and in his statement, he said it had only succeeded in prosecuting three suspected terrorist in more than seven years.
Answering liberal complaints, White House press secretary Robert Gibbs told reporters: "First and foremost, the president does what is in the best security interest of the United States."
For now, the military trials will remain on hold, as they have been since the beginning of his administration, as Obama changes the legal system that is expected to try fewer than 20 of the 241 detainees now being held at Guantanamo.
The president said that immediate rule changes governing the trials will begin to bring them in line with the rule of law, most significantly by altering some rules of allowable evidence. Obama also is asking Congress to change the 2006 law creating the current, on-hold tribunal system to enact more sweeping reforms.
"Military commissions have a long tradition in the United States. They are appropriate for trying enemies who violate the laws of war, provided that they are properly structured and administered," Obama said.
Thirteen Guantanamo detainees - including five charged with helping orchestrate the Sept. 11, 2001, attacks - are already in the tribunal system.
Pentagon lawyers were filing a continuance request with the military commissions judge seeking a 120-day delay in trials to give it time to enact at least the initial rule changes.
The tribunal system was established after the military began taking detainees from the battlefields of Afghanistan in late 2001.
But it immediately came under repeated challenges from human rights and legal organizations, because it denied defendants most of the rights they would be granted in a civilian courtroom or even in a traditional military court martial.
Obama voted for one version of the tribunal law that gave detainees additional rights, but then voted against the more limited 2006 legislation that ultimately became law.
Liberal groups, already stung by Obama's decision on Wednesday to try to block the court-ordered release of photos showing U.S. troops abusing prisoners in Iraq and Afghanistan, were angered again.
"It's disappointing that Obama is seeking to revive rather than end this failed experiment," said Jonathan Hafetz, a national security attorney at the American Civil Liberties Union. "There's no detainee at Guantanamo who cannot be tried and shouldn't be tried in the regular federal courts system. Even with the proposed modifications, this will not cure the commissions or provide them with legitimacy. This is perpetuating the Bush administration's misguided detention policy."
However, the changes Obama ordered are consistent with his past criticism of the Bush system.
-Restrictions on hearsay evidence that can be used in court against the detainees.
-A ban on all evidence obtained through cruel, inhuman or degrading treatment. This would include statements given from detainees who were subjected to waterboarding, a form of simulated drowning.
-Giving detainees greater leeway in choosing their own military counsel.
-Protecting detainees who refuse to testify from legal sanctions or other court prejudices.
When Obama opposed the system that Congress ultimately approved, he called it "sloppy."
"We have rushed through a bill that stands a good chance of being challenged once again in the Supreme Court," Obama said in a Sept. 28, 2006, speech on the Senate floor. "This is not how a serious administration would approach the problem of terrorism."
Later, on the presidential campaign trail in February 2008, Obama described the Guantanamo trials as "a flawed military commission system that has failed to convict anyone of a terrorist act since the 9/11 attacks and that has been embroiled in legal challenges."
The restrictions on evidence almost certainly will result in only a fraction of detainees who ever will go to trial. The rest of the detainees would either be released, transferred to other nations or tried by civilian prosecutors in U.S. federal courts, an official said.
It's also possible that some could continue to be held indefinitely as prisoners of war with full Geneva Conventions protections, according to another senior U.S. official.
The decision to restart the process puts the administration in a race against the clock to conclude commission trials before the Navy prison is closed, by January 2010. If the trials are still going on, the detainees might have to be brought to the United States, where they would receive even greater legal rights.
Since Obama's executive order to close the prison, Republicans have focused on the issue of where the detainees would go - and the new Democratic administration's lack of a plan to deal with them.
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