President Obama signed the massive defense policy bill into law Thursday but used an accompanying statement to say he reserved the right to ignore part of the legislation that prevents him from transferring detainees at Guantanamo Bay, Cuba, to the U.S. mainland.

It’s a standard objection that Mr. Obama, who signed the measure while on family vacation in Hawaii, has raised every year as Congress passes the National Defense Authorization Act, with the president claiming the power to conduct military affairs and to determine where to try cases, and arguing that preventing detainees from being transferred into the U.S. conflicts with his powers under the Constitution.

“For decades, Republican and Democratic administrations have successfully prosecuted hundreds of terrorists in federal court. Those prosecutions are a legitimate, effective and powerful tool in our efforts to protect the nation,” Mr. Obama said in his signing statement. “Removing that tool from the executive branch does not serve our national security interests.”

Mr. Obama also signed the bipartisan budget deal that cleared Congress earlier this month, which eases some of the sequester cuts this year and next year and replaces them with fee increases and other spending cuts spread out over the next decade.

Even that deal’s authors admitted they made a mistake by cutting cost-of-living benefit increases for wounded veterans, and some veterans’ groups had pleaded with Mr. Obama to veto the bill and force Congress to rework it.

Instead, lawmakers have said they’ll come back early next year and try to patch the cuts — though they are already sparring over where to find the money to do so, and the veterans could end up finding themselves competing with the unemployed and others for scarce federal dollars.

The vacationing Mr. Obama signed five other bills Thursday, as he began to clear the decks of last-minute legislation Congress approved before adjourning for the year.

The defense bill almost didn’t pass at all, with Republicans and Democrats fighting over how much debate or amendments to allow in the Senate on the legislation. Finally, lawmakers gave up on a debate altogether, and negotiated a deal with the House, bypassing the Senate for all but a final vote of approval.

The bill creates new safeguards designed to make sure military sexual-assault cases get prosecuted and victims are protected, and it provides pay increases for service members.

It does not, however, include any new move to sanction Iran for that nation’s nuclear program. Mr. Obama had urged lawmakers not to tie his hands while he’s in the midst of international talks with Tehran.

The president only issued a signing statement on the defense bill.

Mr. Obama ran for the White House in 2008 as an opponent of then-President George W. Bush’s practice of issuing signing statements. But in his five years in office Mr. Obama has issued about two dozen of them himself.

This year’s statement actually contains fewer objections than previous defense policy bill statements — in part because the president won some small concessions from Congress.

The new legislation eases some of the tight restrictions that had made it nearly impossible to transfer detainees from Guantanamo Bay to foreign countries. After some heated fighting, Congress agreed to the changes and pushed the bill through the House earlier this month and the Senate late last week.

Despite the improvements, Mr. Obama said there are still too many restrictions on his ability to transfer detainees, including conditions that must be met for transfer, and said those limits still interfere with his constitutional powers.

“The executive branch must have the flexibility, among other things, to act swiftly in conducting negotiations with foreign countries regarding the circumstances of detainee transfers,” Mr. Obama said.

He assured Congress that even without any limits he himself would have made sure not to send detainees home if he wasn’t reasonably sure they would no longer pose a threat or wouldn’t be subjected to torture.

Mr. Obama took office vowing to close the prison at Guantanamo, but has been thwarted at every step by both Democrats and Republicans in Congress, who have said they don’t want detainees brought to the U.S. where they could enjoy more rights, and who say that transferring them to other countries could help some of them return quickly to the battlefield.

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