WASHINGTON — Capitol Hill talk of extending the stopgap measure to fund the federal government is complicating prospects for resolving the annual defense policy bill, according to Sen. John McCain.

McCain, who as the Senate Armed Services chairman is one of "Big Four" lawmakers hammering out the 2017 National Defense Authorization Act, said Tuesday he was confident they would be wrapping up soon. As did House Armed Services Committee Chairman Mac Thornberry. 

Thornberry, R-Texas, called the time frame, "a matter of days," and that the bill would not be wrapped up until December, after the Thanksgiving recess.

After a meeting with the committee's ranking member, Sen. Jack Reed, D-R.I., on Tuesday, McCain indicated contentious policy provisions and the levels of defense funding remain the major sticking points.

"We had a good meeting today and we should be done very soon," said McCain, R-Ariz.

Behind closed doors, leaders from both chambers are debating how to fund the federal government for 2017, whether through one massive omnibus appropriations bill, through a series of "minibus" packages of appropriations, or by extending the current stop-gap continuing resolution into next year to allow President-elect Donald Trump to offer his own 2017 federal budget proposal.

Though the NDAA is the authorization bill, lawmakers try to match the Pentagon spending bill. McCain called the funding question "the hardest part," saying, "We need to discuss that because I understand there are other proposals, like a CR, and we need to find out how it plays into all that."

Thornberry had no preference how the appropriations are packaged, but said he would prefer this Congress pass a 2017 budget this year and avoid a long-term CR the defense department would find disruptive.

"My preference is to finish this year's business now," Thornberry said. "A new administration can always ask for a supplemental if they think it's not enough for defense, but I think it would be good to finish this year's business and start fresh because there is a lot to be done."

"For defense, CRs are always bad, and the longer they are the more damage they do," Thornberry said.

McCain, Thornberry, Reed and HASC Ranking Member Adam Smith, D-Wash., are negotiating defense policy bills that reflect an $18 billion difference in the two chambers’ differing approaches to the emergency Overseas Contingency Operations (OCO) account.

The Senate spending and policy bills support the president's budget, while the House bills redirect $18 billion in OCO — which is exempt from statutory budget caps — for unrequested troops and equipment. The gambit, spearheaded by House Republicans, would leave operations in Afghanistan unfunded to force the next president to request Congress pass supplemental defense spending.

The Obama White House has issued veto threats against the 2017 NDAA over this approach to OCO, as well as a number of reforms to DoD's structure and acquisitions apparatus.

The White House earlier this month requested $5.8 billion in OCO for the Pentagon, but McCain dismissed the amount Tuesday as unsatisfactory.

"We need more than that," McCain said.

Two key policy provisions threaten to derail the NDAA, and according to Thornberry, lawmakers are reassessing such provisions in light of the incoming administration.

The House's No. 2 Republican, Majority Leader Kevin McCarthy, of California, has indicated he will not let the bill proceed unless it contains language to bar an endangered bird called the sage grouse from the federal endangered species list until at least 2025. 

"I think sage grouse [language] should stay in there, should stay in the NDAA, and we should get that done as soon as possible," McCarthy said Monday. 

Federally mandated accommodations for the sage grouse touch energy, mining and ranching interests. Although some House Republicans argue such accommodations would hinder operations at some US military bases, the armed services committee leaders argue the Defense Department has no need for the provision and that it should be excluded from the final bill.

It's unclear whether the language would be needed under a Trump administration that might prioritize commerce and land rights over protections for the bird. When asked, McCain and Thornberry said it was too soon to say.

"We're looking at all those provisions to see what difference a different administration makes," Thornberry said Monday.

On a separate issue, in late October, 42 senators led by Sen. Richard Blumenthal, D-Conn., urged leadership of the House and Senate armed services committees to remove language they say would allow for discrimination based on sexual orientation and gender identity.

An amendment added to the House version of the bill would expand protections and exemptions to "any religious corporation, religious association, religious educational institution, or religious society" that receives a federal contract. 

Senate Democrats argue that the amendment could nullify President Obama's executive order barring federal contractors from discriminating against lesbian, gay, bisexual and transgender individuals—potentially a moot point in NDAA negotiations if Trump decides to revoke the order after assuming office.

Blumenthal, on Tuesday, said he had not heard whether the language remains in the NDAA and indicated Democrats are relying on a threat from the White House to veto the NDAA over the measure.