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WASHINGTON — President Obama set aside his veto threat and late Wednesday signed a defense bill that imposes restrictions on transferring detainees out of military prisons in Afghanistan and Guantánamo Bay, Cuba. But Obama attached a signing statement claiming he has the constitutional power to override the limits in the law.

The move awakened a dormant issue from his first term: his broken promise to close the Guantánamo prison. Lawmakers intervened by imposing statutory restrictions on transfers of prisoners to other countries or into the United States, either for continued detention or for prosecution.

Now, as Obama prepares to begin his second term, Congress has tried to further restrict his ability to wind down the detention of suspected terrorists worldwide, adding new limits in the National Defense Authorization Act of 2013, which lawmakers approved in late December.

The bill extended and strengthened limits on transfers out of Guantánamo to troubled nations such as Yemen. It also, for the first time, limited the Pentagon’s ability to transfer the roughly 50 non-Afghan citizens being held at the Parwan prison at Bagram Air Base in Afghanistan.

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Despite his objections, Obama signed the bill, saying its other provisions on military programs were too important to jeopardize. Early Thursday, the Obama administration released the signing statement in which the president challenged several of its provisions.

For example, in addressing the new limits on the Parwan detainees, Obama wrote that the provision “could interfere with my ability as Commander in Chief to make time-sensitive determinations about the appropriate disposition of detainees in an active area of hostilities.”

He added that if he decided that the statute was operating “in a manner that violates constitutional separation of powers principles, my administration will implement it to avoid the constitutional conflict” — legalistic language that means interpreting the statute as containing an unwritten exception a president may invoke at his discretion.

Saying he continued to believe that closing the Guantánamo prison was in the country’s fiscal and national-security interests, Obama made a similar challenge to three sections that limit his ability to transfer detainees from Guantánamo, either into the U.S. for prosecution before a civilian court or for continued detention at another prison, or to the custody of another nation.

Andrea Prasow, senior counterterrorism counsel and advocate at Human Rights Watch, which supports closing Guantánamo, criticized Obama for not vetoing the legislation. “The administration blames Congress for making it harder to close Guantánamo, yet for a second year President Obama has signed damaging congressional restrictions into law,” she said.

About 166 men remain at the prison.

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