Senate Armed Services Committee Chairman John McCain (R-Ariz.) has been waiting for the administration to put forward a plan for the Guantanamo Bay detention center. (AP Photo/Evan Vucci, File)

A veto-proof majority of the Senate on Tuesday voted in favor of the annual defense authorization bill, sending the measure to the president’s desk amid an ongoing standoff over the Guantanamo Bay detention center.

The measure, which the Senate passed by a vote of 91 to 3, is the product of a long negotiation between the House and Senate. Armed Services Committee leaders in both chambers recently re-negotiated the legislation after President Obama vetoed an earlier version because he objected to the use the of an off-budget war funding account to boost Pentagon spending. A recent broader budget deal resolved that issue and the new, $607 billion measure was endorsed by leaders of both parties. The House passed the bill last week by a vote of 370 to 58.

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But the strong vote in favor of the bill does not resolve lingering questions over the fate of Guantanamo Bay, which the administration had hoped to shutter through the defense policy bill.

The National Defense Authorization Act (NDAA) instead includes, over the administration’s objections, a ban on transferring any Guantanamo detainees to American soil or the countries of Somalia, Libya, Syria and Yemen. There are still over 100 detainees at the facility, most of whom have not been slated for transfer.

White House Spokesman Josh Earnest said on Tuesday that the president will likely sign the bill, but he made clear that doesn’t indicate a change in the administration’s position that the detainee facility should be closed.

“The president believes that closing that prison is a national security priority,” Earnest said, while later adding that despite the differences over Guantanamo “there are a number of provisions in the NDAA that are important to running and protecting the country and so that’s why I would expect that you would see the president sign the NDAA when it comes to his desk .”

[Opinion: Keep Guantanamo open]

This year’s defense authorization bill was likely the last vehicle the administration could have used to compel Congress to vote on the question of shuttering Guantanamo. Senate Armed Services Committee Chairman John McCain (R-Ariz.) earlier this year offered the administration the bill as a potential route to putting the Guantanamo question before Congress. Next year’s bill isn’t likely to be ready for a vote until close to the November elections, when lawmakers are unlikely to want to address a politically touchy subject like Guantanamo Bay.

Earnest pushed back against the idea that the administration has missed the opportunity to get Congress to consider closing the facility.

“I don’t think this has any material impact on our ability to put together and send to Congress a thoughtful, carefully considered plan for closing the prison at Guantanamo Bay, and a plan that we believe merits the strong support of both Democrats and Republicans in the Congress,” he said. “That will, however, require Democrats and Republicans in the Congress to put the national interest ahead of their much more narrow and, in comparison, trivial political interests.”

With few legislative options left, however, Republicans are concerned that the Obama administration will try to go around Congress and close Guantanamo through executive action.

[For Congress, Guantanamo closure plan might come too late]

The administration, so far, has not threatened to act on its own authority, but officials have not expressly ruled it out.

Some congressional Democrats don’t seem to be that alarmed by the prospect that Guantanamo could be closed without Congress’ help.

“Well, they set it up by executive action, there was no authorization of Guantanamo,” said Sen. Dianne Feinstein (D-Calif.) “So you know, what you can build, you can take apart too, it seems to me.”

Republicans believe they have taken the needed steps to ultimately block such a move.

Congress has included language in the authorization bill “for years now” to prevent the president from closing the facility without an act of Congress, McCain said, giving the legislative branch leverage with the courts.

“Just like a federal judge has just stayed his orders on immigration,” McCain said, referencing a federal appeals court’s Monday decision against Obama’s plan to protect up to 5 million undocumented immigrants from deportation. “He doesn’t respect the Constitution anymore.”

McCain said he would give the administration’s Guantanamo plan a close look when released, but was not expecting it to be comprehensive or conclusive.

“If it’s a whole set of different options,  I don’t have to look very hard,” he said. “Because a plan is a plan; a whole bunch of different options are different options, not a plan.”