WASHINGTON — President Barack 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 Guantanamo Bay, Cuba. But Obama attached a signing statement claiming that he had constitutional power to override the limits in the law.

Obama’s move awakened a dormant issue from his first term: his broken promise to close the Guantanamo 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.

The bill, approved in late December, extended and strengthened limits on transfers out of Guantanamo to troubled nations like Yemen, where the bulk of remaining low-level detainees cleared for repatriation are from. It also, for the first time, limited the Pentagon’s ability to transfer the roughly 50 non-Afghan citizens being held at Bagram Air Base in Afghanistan at a time when the future of U.S. detention operations there is murky.

Early Thursday, shortly after midnight, the White House released the signing statement. Saying that he continued to believe that closing the Guantanamo 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 Guantanamo, either into the United States for prosecution before a civilian court or for continued detention at another prison, or to the custody of another nation.