Several officials said that it was not certain, even from inside the government, what Mr. Obama’s intentions were. While the signing statement fell short of a veto, they said its language appeared intended to preserve some flexibility for the president to make a decision later about whether to make a new push to close the Guantánamo prison amid competing policy priorities.

Andrea Prasow, senior counterterrorism counsel at Human Rights Watch, which advocates closing Guantánamo, criticized Mr. Obama for not vetoing the legislation despite his threat to do so.

“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. “The burden is on Obama to show he is serious about closing the prison.”

About 166 men remain at the prison.

Signing statements are official documents issued by a president when he signs bills into law that instruct subordinates in the executive branch about how to carry out the new statutes. In recent decades, starting with the Reagan administration, presidents have used the device with far greater frequency than in earlier eras to claim a constitutional right to bypass or override new laws.

The practice peaked under President George W. Bush, who used signing statements to advance sweeping theories of presidential power and challenged nearly 1,200 provisions over eight years — more than twice as many as all previous presidents combined.

The American Bar Association has called upon presidents to stop using signing statements, calling the practice “contrary to the rule of law and our constitutional system of separation of powers.” A year ago, the group sent a letter to Mr. Obama restating its objection to the practice and urging him to instead veto bills if he thinks sections are unconstitutional.

As a presidential candidate, Mr. Obama sharply criticized Mr. Bush’s use of the device as an overreach. Once in office, however, he said that he would use it only to invoke mainstream and widely accepted theories of the constitutional power of the president.