But the Pentagon spending bill kept two sets of restrictions on the president’s powers to close the prison camps, something he had declared by Executive Order on Jan. 22, 2009 would happen in the first year of his first administration:

•  One portion forbids the use of federal funds to transfer Guantánamo detainees to U.S. soil for any reason, including a federal criminal trial.

•  The other maintains restrictions on executive branch authority to transfer detainees to a foreign country and have all-but frozen transfers from the base. Only those detainees who die in custody or who get court release orders can leave without a Defense Department waiver and certification to Congress.

The last two detainees to leave were a Yemeni man who the military says committed suicide by overdose in a maximum-security lockup and convicted war criminal Omar Khadr to a prison in his native Canada under a diplomatically negotiated plea deal.

Early in Obama’s presidency, diplomats negotiated transfer agreement to third countries for resettlement (Germany, Bermuda, El Salvador, Palau are some examples). But the diplomatic talks ground to a halt because of Congress’ restrictions on transfers.

The Justice Department has notified the federal court that it has cleared 55 captives for release, many of them Yemenis and Syrians who can’t be safely repatriated to their homelands. They have nowhere to go, so they remain in detention because of the restrictions.

Obama’s signing statement casts the restrictions as an encroachment on executive powers.

By forbidding federal trials for Guantánamo captives, he said, the law he signed “substitutes the Congress’s blanket political determination for careful and fact-based determinations, made by counterterrorism and law enforcement professionals, of when and where to prosecute Guantánamo detainees.

“Removing that tool from the executive branch undermines our national security. Moreover, this provision would, under certain circumstances, violate constitutional separation of powers principles.”

And echoing past statements, Obama also left open the possibility that administration attorneys might interpret the restrictions as overreaching and inapplicable.

“My administration will interpret these provisions as consistent with existing and future determinations by the agencies of the executive responsible for detainee transfers,” Obama said. “In the event that these statutory restrictions operate in a manner that violates constitutional separation of powers principles, my administration will implement them in a manner that avoids the constitutional conflict.”

Prison camp critics issued statements of disappointment that the president had signed the legislation and in some instances urged him to use his executive powers to ignore the limits.

“The president needs to act now if he’s going to close Guantánamo within his second term,” said Dixon Osburn of the legal advocacy group Human Rights First. “It’s time to put a senior White House official in charge and begin transferring cleared detainees.”

A White House pool report from Honolulu said Obama signed the Pentagon spending law personally — unlike the tax bill that averted the U.S. from going over the fiscal cliff, which Obama had signed in Washington with an autopen. Congress delivered the NDAA bill over the weekend, and the traveling White House brought it to Hawaii with Obama.