The move would affect the five detainees charged with having played key roles in the September 11, 2001 attacks on New York and Washington, including Khalid Sheikh Mohammed, who has been accused of planning the attacks.
Human rights and civil liberties groups were critical of the decision, saying the tribunal system should be scrapped.
"It's disappointing that Obama is seeking to revive rather than end this failed experiment," Jonathan Hafetz, a lawyer at the American Civil Liberties Union, said.
|Obama has already faced criticism
over the move [AFP]
"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."
A total of 13 of the 241 detainees held at Guantanamo Bay are currently in the military tribunal system, which has only convicted three prisoners in eight years.
Obama has been critical of the military tribunal system in the past, describing them in June 2008 as an "enormous failure".
But a US official said that the president had consistently backed military commissions as an option to try detainees, but believed the version used by the administration of George Bush, the previous US president, did not have protections.
The decision to restart the process means trials would have to finish before the Guantanamo facility is closed in January 2010, or the detainees would need to be transferred to the US mainland, where they would have more legal rights.
Obama has come under increasing pressure over the treatment of al-Qaeda suspects after memos written by Bush-era legal officials released last month that argued that tactics including waterboarding, which simulates the sensation drowning, were not torture.