President Barack Obama signed the National Defense Authorization Act of 2013 on Wednesday, despite his own threat to veto it over prohibitions on closing the Guantanamo Bay prison camp.

Civil liberties advocates had roundly criticized the bill over Guantanamo and a separate section that could allow the military to indefinitely detain American citizens on suspicions of supporting terrorism. Just as he did with last year's version of the bill, however, Obama decided that the need to pass the NDAA, which also sets the armed forces' $633 billion budget for the 2013 fiscal year, was simply "too great to ignore," according to a presidential signing statement released in the early morning hours Thursday.

Members of the human rights coalition that had urged Obama to follow through on his veto threat blasted his decision as a cave to congressional Republicans.

"President Obama has utterly failed the first test of his second term, even before inauguration day,” American Civil Liberties Union Executive Director Anthony Romero said in a statement. “His signature means indefinite detention without charge or trial, as well as the illegal military commissions, will be extended.”

"It's the second time that the president has promised to veto a piece of a very controversial national security legislation only to sign it," said Shahid Buttar, executive director of the Bill of Rights Defense Committee. "He has a habit of promising resistance to national security initiatives that he ultimately ends up supporting and enabling."

After the president issued his veto threat in November, a House-Senate conference committee made one minor change: it shortened the length of the bill's prohibition on transferring Guantanamo detainees to the U.S. to one fiscal year, instead of the open-ended ban in the original Senate version.

Obama's signing statement did reiterate his opposition to restrictions on when he can move prisoners out of the Guantanamo camp. Such statements signal how a president plans to put a law into effect but do not have the force of law themselves, leaving future administrations to make their own interpretations.

As Politico's Josh Gerstein notes, however, Obama’s recent signing statement significantly toned down his promises to reverse parts of the bill he objected to. Last year, Obama’s signing statement said his administration had “worked tirelessly to reform or remove the provisions” he found objectionable. Obama’s latest statement made no such claim.

Obama also allowed provisions of the law that require his administration to place certain terrorism suspects into military custody to stand without comment, though the administration’s interpretation of that section of the law renders it nearly irrelevant. Under procedures released by the White House in February, the military custody requirement can be waived in a wide variety of cases, including if the suspect’s home country objects to military custody; if the suspect is arrested for conduct conducted in the U.S.; and if the suspect is originally charged with a non-terrorism offense. The administration also claimed the military custody requirement didn’t apply in cases where the suspect was originally arrested by state or local law enforcement, when a transfer to military custody could interfere with efforts to secure cooperation or confession or when a transfer would interfere with a joint trial.

Obama's signature caps an intense sequence of events for opponents of indefinite detention. In November, a bipartisan group of senators amended their chamber's NDAA bill to prohibit the military from detaining American citizens on American soil. But when the House and Senate met to reconcile their versions of the NDAA, that amendment was stripped out behind closed doors.

"The president seemed to have nothing to say about that," Buttar said. "The whole process, quite frankly, was a reflection of the worst parts of Washington -- the institutional dysfunction, the lack of historical memory, the unwillingness to consider relatively limited reforms that would make these powers responsible and limited."

Outside of Congress, civil liberties groups are pushing forward with a lawsuit against the indefinite detention provisions of the NDAA on the grounds that they are unconstitutional. Supreme Court Justice Ruth Bader Ginsburg denied their efforts to reinstate an injunction against indefinite detention on Dec. 14, but the case against the law is still proceeding in the Second Circuit Court.

Demonstrations and political pressure around Guantanamo, meanwhile, will also continue. Civil liberties groups argue that despite the provisions in the NDAA, the president may still be able to close the detention camp or at least free some of the inmates there. Still, they were disappointed by his signature.

"It's not encouraging that the President continues to be willing to tie his own hands when it comes to closing Guantanamo," Dixon Osburn, the director of Human Rights First's Law and Security Program, said in a statement. "The injustice of Guantanamo continues to serve as a stain on American global leadership on human rights."

Jan. 11 marks the 11th anniversary of the prison camp's opening there.

Michael McAuliff contributed reporting.

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