Obama’s decision to drop the veto threat disappointed and angered civil-liberties and human rights groups who had been urging him to block the legislation. Amnesty International’s Tom Parker said the bill “enshrines the war paradigm that has eroded the United States’ human rights record and served it so poorly over the past decade as the country’s primary counterterrorism tool,” adding that the president “has abandoned yet another principled position with little or nothing to show for it.”

Senate Intelligence Committee Chairwoman Dianne Feinstein (D-Calif.), who had led one of several unsuccessful efforts to strip the provisions from the legislation, said she would introduce legislation to bar indefinite military detention of U.S. citizens in all cases.

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The legislation also includes a provision requiring tougher sanctions against those doing business with Iran’s Central Bank, something which the White House also tried to weaken but had broad support among lawmakers. Also included is a provision to freeze $700 million in counterinsurgency aid to Pakistan until Islamabad cracks down on the spread of improvised explosive devices and the material to make them into Afghanistan.

It also would make the head of the National Guard Bureau a member of the Joint Chiefs of Staff, the first change in composition to the president’s top military advisory body in 25 years. Attempts to do that in past years had been stripped from the bill in the face of Pentagon opposition, but this year broad support from lawmakers and the Guard’s high-profile role in Iraq and Afghanistan outweighed the united opposition of the Joint Chiefs and Defense Secretary Leon Panetta.

The Guard’s current top officer, Air Force Gen. Craig McKinley, whose term expires in November 2012, would presumably become the first to take his seat on the Joint Chiefs if the legislation becomes law.

The final legislation also substantially weakened House-passed measures designed to prevent the Pentagon from recognizing gay marriage in the wake of the repeal of “don’t ask, don’t tell,” including only a provision allowing military chaplains to opt-out of performing such ceremonies if their beliefs oppose them.

In all, the bill authorizes $670 billion in spending for the Defense Department, along with Energy Department nuclear weapons programs. The money is tied up in a $1 trillion-plus fiscal 2012 omnibus being negotiated by congressional leaders.