Backing down on a threatened veto, President Obama signed into law a $633.3 billion defense bill with an attached statement in which he serves notice to Congress that he will interpret the law as he sees fit on issues ranging from the transfer of terrorism detainees to military chaplains’ objections to the new policy on gay service members.

Mr. Obama said in a “signing statement” late Wednesday that he agrees with the “vast majority” of provisions in the 680-page law. But he added, “I do not agree with them all.” He earlier had issued a veto threat to Congress if some of the objectionable provisions in the bill survived.

In spite of many veto threats in his first term, Mr. Obama has vetoed only two bills, both relatively inconsequential measures.

When he ran for the presidency in 2008, Mr. Obama criticized President George W. Bush for the Republican’s use of signing statements, arguing that Mr. Bush too often was ignoring the will of Congress.

The president said in his new message that he objects to Section 1027 of the law, which renews the prohibition against transferring terror detainees from the Guantanamo Bay detention center in Cuba to the United States for any purpose.

“I continue to oppose this provision, which 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 Guantanamo detainees,” Mr. Obama wrote. “This provision would, under certain circumstances, violate constitutional separation of powers principles. 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.”

The issue of transferring detainees to the U.S. mainland has been a point of contention almost since the beginning of Mr. Obama’s presidency, when he served notice that he intended to close the detention center. Lawmakers in both parties have objected to earlier administration plans, since abandoned, to hold trials for some terrorism suspects in the U.S.

Mr. Obama, who ended the military’s long-standing “don’t ask, don’t tell” policy, also cited as “unnecessary and ill-advised” a provision in the law that gives service members and military chaplains the legal right to oppose homosexuality and the gay lifestyle as long as their opposition does not interfere with good order and discipline in the military.

“The military already appropriately protects the freedom of conscience of chaplains and service members,” Mr. Obama said. “My administration remains fully committed to continuing the successful implementation of the repeal of ‘don’t ask, don’t tell,’ and to protecting the rights of gay and lesbian service members.”

The president also said he objects to a provision that blocks proposed increases in health insurance fees for service members. He said it could result in deeper cuts to military personnel.

The Defense Department has proposed significant increases in Tricare fees for working-age retirees and their families, but the new law blocked that effort, limiting fee increases to the increase in the cost of living.

“By failing to allow some of these cost savings measures, the Congress may force reductions in the overall size of our military forces,” Mr. Obama said.

The bill also tightens penalties on Iran and beefs up security at U.S. diplomatic posts after the deadly attack in Benghazi, Libya, last September.

In spite of his veto threat, Mr. Obama said he signed the law because “the need to renew critical defense authorities and funding was too great to ignore.”

In addition, the measure contains cuts in defense spending to which the president and congressional Republicans agreed in August 2011.

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