"From the beginning of my administration, the United States has worked to bring terrorists to justice consistent with our commitment to protect the American people and uphold our values," Obama said in a statement issued by the White House. "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.
"I strongly believe that the American system of justice is a key part of our arsenal in the war against al-Qaida 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."
Attorney General Eric Holder said in a statement the administration still maintains "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."
Holder said the government would continue to pursue cases against the detainees and added the president's executive order "strengthens the legal framework under which we will continue to detain those individuals who are at war with our country and who pose a significant threat to the security of the United States."
Secretary of State Hillary Clinton said in a statement the administration was reaffirming it will follow Geneva Convention protocols in treating detainees humanely.
"These steps we take today are not about who our enemies are, but about who we are: a nation committed to providing all detainees in our custody with humane treatment," Clinton said. "We are reaffirming that the United States abides by the rule of law in the conduct of armed conflicts and remains committed to the development and maintenance of humanitarian protections in those conflicts."
The freeze on prosecutions at Gitmo has been in place since January 2009. There are about 170 prisoners at the facility, down from 242 when Obama took office, the Los Angeles Times said. The White House has said the president still intends to close the prison, the newspaper said.
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