CBS News correspondent Kimberly Dozier reports that the president says these will not be your Bush-era tribunals, promising a new system that guarantees more legal rights for detainees.
Mr. Obama said the changes were designed to give defendants stronger legal protections, such as a ban on evidence "obtained through torture, or by using cruel or degrading interrogation methods," like waterboarding; limiting use of hearsay evidence; granting the accused more say in who represents them; and protecting detainees who refuse to testify from legal sanctions.
But his action was almost instantly denounced by critics who called the new tribunals "Bush Lite," reports Dozier.
During his presidential campaign, Mr. Obama was highly critical of the commissions used by the Bush administration.
"By any measure, our system of trying detainees has been an enormous failure," he said last June 18.
And one of his first actions as president was setting in motion the closing of Guantanamo Bay prison within 12 months.
Re-opening these military tribunals may also delay the closing of Guantanamo, says Dozier. The earliest the trials of 13 defendents (9 of whom are charged with helping orchestrate the September 11 terror attacks) can resume is September. That would give prosecutors about four months to finish before the end of the year, because these military tribunals cannot be held back in the United States.
The rest of the 241 Guantanamo detainees will either be released, transferred to other countries, tried in civilian U.S. federal courts or, potentially, held indefinitely as prisoners of war with full Geneva Conventions rights.
"This is the best way to protect our country, while upholding our deeply-held values," Mr. Obama said in a three-paragraph White House statement.
The administration said he was not embracing the Bush-era system because it would be so significantly changed.
Human rights groups disagreed.
"In one swift move, Obama both backtracks on a major campaign promise to change the way the United States fights terrorism and undermines the nation's core respect for the rule of law," said Amnesty International executive director Larry Cox.
"As a constitutional lawyer, Obama must know that he can put lipstick on this pig - but it will always be a pig," said Zachary Katznelson, legal director of Reprieve, a London-based legal action charity that represents 33 Guantanamo detainees.
Critics called it a return to a second class system of justice for cases without enough evidence for a federal trial.
David Remes, a attorney for 18 detainees, said, "It's a prosecutor's dream, it's a defendent's nightmare."
The White House disagrees: "The notion that this is the same vehicle is simply, it's simply not true," said Press Secretary Robert Gibbs.
Mr. Obama's announcement was greeted more warmly on Capitol Hill, where he will need broad support to quickly push through tribunal changes. The White House hopes to do so before mid-September, when a new 120-day freeze the president put on the cases Friday runs out.
The Democratic chairman of the Senate Armed Services Committee, Carl Levin, D-Mich., called the changes "essential in order to address the serious deficiencies in existing procedures." Senate GOP Leader Mitch McConnell said the announcement was an "encouraging development."
"It's a difficult legal situation, and I think this is really the only rational choice to make," said Sen. Sam Brownback, R-Kan., who opposes bringing detainees to the military's maximum security prison located in his state.
The tribunal system was established after the military began taking detainees from the battlefields of Afghanistan in late 2001. But the process immediately and repeatedly was challenged by human rights and legal organizations for denying defendants rights they would be granted in most other courts.
As a senator, Mr. 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.
Friday's changes restore some of those rights.
Veterans of the Bush White House say Mr. Obama faced the same hard choice their boss did: Finding a way to keep dangerous men in jail.
"Call it a war on terror, call it what you like, but if there is an ongoing fight, then the openness, the due process that is normally attached to a criminal legal process is difficult," said CBS News national security analyst Juan Zarate.
The latest delay, however, means Mr. Obama could face an uncomfortable choice as the clock runs out on his self-imposed January 2010 deadline to close Guantanamo.
His administration will have only four months to finish the nine trials before then, or risk moving the cases to the United States if they are still under way. If that happens, the detainees would be given even greater legal rights than they have at Guantanamo - and more than Mr. Obama wants to give.
Asking Congress to change the 2006 commissions law could create longer delays. Lawmakers, leery that the detainees could be brought to the U.S., already have held up funding for closing the prison until the White House outlines details of how it would happen.
President Obama could roll back the January 2010 deadline, which he imposed on his second day in office. That could throw in doubt his campaign promise to shut down the prison and, at the least, highlight his struggle to reverse Bush-era national security policies that damaged America's image worldwide and stoked recruitment among insurgents.
Clive Stafford Smith, who represents several current and former detainees, was surprised that the Obama administration plans to restart the trials at Guantanamo instead of elsewhere. "There is zero chance that the military commissions could be over by January, so that cannot possibly be the plan," he said.
Navy Lt. Richard Federico, who represents two Guantanamo detainees charged before the military commissions, including alleged 9/11 plotter Ramzi bin al Shibh, also doubted cases could be completed by January. Litigation over the legality of the new rules "will certainly incur additional delay," Federico told The Associated Press.
The White House says this is not a departure from campaign promises. They said they always had a problem with the way tribunals were carried out, not the idea of military commissions overall.
Don Baer, who served as Director of Strategic Planning and Communications in the Clinton White House, said Mr. Obama is "not technically" breaking a campaign promise.
"He's modifying where he was back last August," Baer said on CBS' The Early Show Saturday Edition. "It's an indication that governing is a more complicated and complex situation … than campaigning is.
"I suspect it's a change of direction that will help the president because it underscores he's governing in a way that is going to keep the country safer."
Baer suggested that presidents get more information about security threats than do presidential candidates, and so Mr. Obama was simply acting on what he knew. "Given what he knew at the time, he was being responsible. Given what he knows today, he's being even more responsible."
Todd Harris, who was John McCain's communications director during his 2000 White House run, said Mr. Obama was simply being realistic and applauded his decision.
"But let's be honest here: this is a reversal," he said on The Early Show. "He campaigned as someone who was going to close the book on Bush-era terrorism techniques, but seems to be writing a new chapter. It's not just the military commissions; it's continued support for the Bush administration's warrantless wiretap programs, keeping Guantanamo Bay open, refusing to release the photos of depicted abuse.
"Time after time, as Don said, the administration is finding that it's a lot harder to actually implement these campaign promises than it was to make them back in the campaign."