With President Obama’s second term about to begin, one of his administration’s first promises, that it would close the military detention center at Guantanamo Bay, Cuba, looks all but abandoned after he signed a defense bill late Wednesday that includes an array of tough restrictions on the transfer of detainees out of the facility.

Obama had threatened to veto the $633 billion National Defense Authorization Act but signed it, as he did last year, with a statement criticizing sections of the bill that he said are “unwarranted restrictions on the executive branch’s authority” by Congress.

In the case of Guantanamo, the legislation bars the transfer of detainees into the United States for any purpose, including trials in federal court. It also requires the defense secretary to meet rigorous conditions before any detainee can be returned to his own country or resettled in a third country.

Plea agreement rules

The measure may also have the little-noticed effect of reducing the number of prosecutions in military commissions at Guantanamo by making it more difficult for the government to reach plea agreements with defendants.

Until now, five of the seven completed prosecutions at Guantanamo have come through plea agreements, and a number of other detainees are anxious to strike deals with military prosecutors in return for a certain date of release, military officials and defense attorneys said.

Previously, the government could simply transfer out a detainee who had pleaded guilty and served his time without meeting stringent congressional reporting requirements. But the 2013 act removes that exception and requires the defense secretary to certify that such detainees will not be a future threat. The Pentagon has not been willing to provide that kind of certification for any detainee, including those cleared for release.

“Removing the carve-out for plea agreements really weakens an already illegitimate military commission system,” said Laura Pitter, a counterterrorism adviser at Human Rights Watch. “How is the government going to make plea agreements with detainees when it is not even authorized to follow though on promises already made?”

But military officials said the government can still push through a detainee’s release. And defense lawyers may still calculate that the prospect of release, however distant, is worth accepting a deal.

Obama issued a signing statement with the law that asserted his constitutional right to override provisions that he believe infringe on the powers of the executive.

“The Congress has designed these sections, and has here renewed them once more, to foreclose my ability to shut down the Guantanamo Bay detention facility,” Obama said. “I continue to believe that operating the facility weakens our national security.”

Critics: Obama’s failure

Obama’s critics in the human rights community said that he should have vetoed the bill and that by signing it, he was again signaling his unwillingness to invest political capital in a fight to close the detention center.

“President Obama has utterly failed the first test of his second term, even before Inauguration Day,” said Anthony Romero, executive director of the American Civil Liberties Union. “He also has jeopardized his ability to close Guantanamo during his presidency.”

The law also for the first time restricts the administration’s ability to repatriate about 50 non-Afghans held by the United States in Afghanistan’s Parwan province. Obama said that “decisions regarding the disposition of detainees captured on foreign battlefields have traditionally been based upon the judgment of experienced military commanders and national security professionals without unwarranted interference by members of Congress.”

There are 166 detainees remaining at Guantanamo, but the process of transferring any of these men home has ground to a halt. There are 30 non-Yemenis cleared for release, including three Chinese Uighurs ordered released by federal courts. The administration has suspended all transfers to Yemen; 56 Yemenis could be transferred if security in Yemen improves, U.S. officials said.

Human rights activists said the administration could restart the transfer process if the White House urged the Pentagon to start issuing the certifications required by Congress regardless of the political fallout.

“Indefinite detention without trial at Guantanamo is illegal, unsustainable and against U.S. national security interests, and it needs to end,” said Andrea Prasow, senior counterterrorism counsel and advocate at Human Rights Watch. “But the administration should not continue to just blame Congress. President Obama should follow through on his earlier commitments and make the effort to overcome the transfer restrictions.”