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The announcement comes more than two years after Obama signed an executive order order Guantanamo Bay to close by January 2010. A White House fact sheet acknowledged that in recent months, "some in Congress have sought to undermine" the process developed by the Departments of Justice and Defense to "determine which system - military or civilian - is most appropriate based on the nature of the evidence and traditional principles of prosecution."
The White House said it would continue to "vigorously defend the authority of the Executive to make these well- informed prosecution decisions, both with respect to those detainees in our custody at Guantanamo and those we may apprehend in the future."
"A one-size-fits-all policy for the prosecution of suspected terrorists, whether for past or future cases, undermines our Nation's counterterrorism efforts and harms our national security," the White House fact sheet said.
It was not immediately clear what the order meant for the Khalid Sheikh Muhammad trial, but Carol Rosenberg of the Miami Herald reported that the White House was hosting a conference call this afternoon for families of victims of the Sept. 11 attacks in which Muhammad has been implicated.
Attorney General Eric Holder said in a statement that it is "essential that the government have the ability to use both military commissions and federal courts as tools to keep this country safe."
"Unfortunately, some in Congress have unwisely sought to undermine this process by imposing restrictions that challenge the Executive Branch's ability to bring to justice terrorists who seek to do Americans harm," Holder said. "We oppose those restrictions, and will continue to seek their repeal."
But Holder said it was important for military commissions to resume. "For the remaining cases the Guantanamo Review Task Force deemed suitable to pursue for prosecution, we will continue to work, along with the Department of Defense, to ensure that justice is done as swiftly as possible."
The executive order signed by Obama said that each detainee at Guantanamo would have an initial review within one year. The order said it was "intended solely to establish, as a discretionary matter, a process to review on a periodic basis the executive branch's continued, discretionary exercise of existing detention authority in individual cases."
"It does not create any additional or separate source of detention authority, and it does not affect the scope of detention authority under existing law. Detainees at GuantÃ¡namo have the constitutional privilege of the writ of habeas corpus, and nothing in this order is intended to affect the jurisdiction of Federal courts to determine the legality of their detention," the order states.
The executive order says that the Attorney General and Secretary of Defense "shall continue to assess whether prosecution of the detainee is feasible and in the national security interests of the United States, and shall refer detainees for prosecution, as appropriate."
Obama said in a statement that United States "has worked to bring terrorists to justice consistent with our commitment to protect the American people and uphold our values."
"Today, I am announcing several steps that broaden our ability to bring terrorists to justice, provide oversight for our actions, and ensure the humane treatment of detainees," Obama said. "I strongly believe that the American system of justice is a key part of our arsenal in the war against al Qaeda and its affiliates, and we will continue to draw on all aspects of our justice system - including Article III Courts - to ensure that our security and our values are strengthened. Going forward, all branches of government have a responsibility to come together to forge a strong and durable approach to defend our nation and the values that define who we are as a nation."
A spokesman for the Justice Department referred calls to the Defense Department and to the White House. A spokeswoman at the Defense Department did not immediately return a call requesting comment.
Read the executive order here.
[Ed. Note: this story has been updated.]