The move seems an attempt to strike a middle ground, as administration critics on the left want the commissions ended and detainees tried in federal court, while those on the right believe the commission system should remain unaltered.
White House changes to the commissions would, among other things, ban evidence obtained through cruel treatment and restrict prosecutors' use of hearsay evidence.
"I believe that Obama is attempting to be responsive to criticisms of the military commissions," says Carl Tobias, a University of Richmond law professor. "Some of the sharpest complaints were about the [previous allowed use] of hearsay evidence."
The move comes at a time when the administration's handling of detainees is coming under increasing scrutiny in Washington.
Members of Congress are pressuring administration officials to figure out what they're going to do with the remaining detainees at the detention camp at Guantánamo Bay, Cuba. Many lawmakers from both parties are adamant that they do not want Guantánamo detainees transferred to federal facilities within their states.
The prison is to be closed by January 2010.
"No final decision has been made with regard to what is going to happen to those 241 people who are in Guantánamo, those who would be eligible for release or transfer.... We're still in the process of trying to make the determination about who's going to be prosecuted [and] who is eligible for transfer or release," said Attorney General Eric Holder at a House Judiciary Committee hearing on Thursday.
Meanwhile, House Speaker Nancy Pelosi charged Thursday that the Central Intelligence Agency misled her about the use of waterboarding in the interrogation of terror detainees. And human rights groups are dismayed about the Obama administration's recent reversal of its position on making public photos that depict detainee abuse by US personnel overseas.
"The Obama administration's adoption of the stonewalling tactics and opaque policies of the Bush administration flies in the face of the president's stated desire to restore the rule of law, to revive our moral standing in the world and to lead a transparent government," said Anthony Romero, executive director of the American Civil Liberties Union, in a statement Wednesday about the photo decision.
It is in the context of this heated atmosphere that Mr. Obama has decided to retain the military commission system, with modifications.
Obama said in a statement released Friday that restarting the modified military tribunals for a small number of terrorist suspects "is the best way to protect our country, while upholding our deeply held values."
Under the Bush system, hearsay evidence had been allowed in the commissions, unless the defendant could prove it was unreliable. Obama is proposing to flip that responsibility, by disallowing hearsay unless the prosecution can prove it is reliable.
Hearsay, or evidence heard secondhand, is generally admissible in civilian US courts only under certain restrictive conditions.
The Obama administration's changes will allow detainees more flexibility in choosing their lawyers. They will also ban all evidence obtained through cruel, inhuman, or degrading treatment. This probably would bar statements coerced through waterboarding, stress positions, and some other controversial Bush-era interrogation techniques.
These immediate rule changes would be carried out by executive order, Obama said. He also asked Congress to change the 2006 law on which the current tribunal system is based, so as to make more sweeping reforms in the future.
Obama is now in the position of reviving a system that he criticized as a senator and presidential candidate.
As he changes the commissions to make them more like civilian trials, he will get closer and closer to an obvious problem, says Professor Tobias of the University of Richmond.
"You might eventually say, 'What is the point?' " he says. "Why not just try these detainees in federal court?"
But trials for terror suspects in US civilian courts have proved difficult in the past – and might be especially so for suspects captured overseas and long held at the Guantánamo prison.
The administration might worry about being forced to divulge classified national-security information in a civilian trial. The question of torture might also loom larger.
"My guess is the administration does not want these trials [in a civilian venue] because they are going to be very difficult," says Hurst Hannum, a professor of international law at Tufts University in Medford, Mass.
In principle, it is possible that the military tribunals could meet minimum international standards of justice, Professor Hannum says. But that might be seen only as they proceed.
"The devil is in the details," he says.