WASHINGTON — (CNN) Congressional Republicans are using the short term government spending bill to expedite a vote on retired Gen. James Mattis, President-elect Donald Trump’s nominee to lead the Defense Department.

Mattis, who retired from the military three years ago, and who was formally nominated Tuesday, needs a special waiver from Congress to serve as the top civilian at the Pentagon. A World War II-era law aimed at preserving civilian control over the military bars those who served in the military in the last seven years from leading the Defense department.

Because Republicans are anxious to ensure Mattis is positioned to be confirmed as close as possible to January 20 — Inauguration Day — they added language to the stopgap funding bill that imposes time limits on the debate over the waiver.

Federal agencies will run out of money at midnight this Friday, but leaders of the House and Senate plan to vote on the bill and send it to President Barack Obama in time to head off any shutdown.

The House is expected to vote first on Thursday and if approved the Senate will take the bill up soon after it is sent over.

The Senate is expected to take up the legislation shortly after his confirmation hearings next month and the provisions ensure the bill can move in a timely fashion to the Senate floor. Republicans had hoped also to lower the threshold from 60 to 51 the votes needed to advance the waiver measure to avoid a Democratic filibuster in the Senate. But after some Democrats balked, the GOP agreed to measures they hope will speed up the confirmation process.

Even though Mattis has been praised by members of both parties, some Democrats have stated they publicly oppose him taking the job because they want to preserve the current system that prevents recent military leaders for ascending to top leadership posts of the Defense Department.

Mattis formally accepted Trump’s nomination at a rally in Fayetteville, North Carolina, saying that he looks forward to serving in the role.

“I look forward to being the civilian leader so long as the Congress gives me the waiver and the Senate votes to content,” Mattis said.

When Mattis stepped off staged, Trump told the audience, “What a great guy, he’s going to incredible … He’ll get that waiver, right? Oh, if he didn’t get that waiver there are going to be a lot of angry people.”

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House Appropriations Chairman Hal Rogers stressed that the bill, which extends current funding levels until April 28, 2017, avoids a shutdown although he stressed he wants to prevent such short-term bills in the next Congress.

“This legislation is just a Band-aid, but a critical one. It will give the next Congress the time to complete the annual Appropriations process, and in the meantime, take care of immediate national funding needs.”

With the increased costs of securing Trump at his midtown Manhattan high rise — costing $1 million a day to protect the President-elect as well as his children and their families — GOP and Democratic leaders added $7 million in the bill to reimburse New York City police and other agencies. New York City Mayor Bill de Blasio and the Obama administration submitted a request for $35 million from the federal government to defray the costs.

Some Democrats were disappointed more money wasn’t included to help local authorities.

“Republicans’ failure to fully reimburse NYPD for its efforts to protect President-elect Trump is beyond disappointing. The $7 million in funding that this bill does provide must be considered a down payment on the way to making NYC whole,” Rep. Nita Lowey, the top Democrat on the Appropriations panel, said in a written statement to CNN.

“New York City taxpayers should not be on the hook for 80% of the national bill to protect our president-elect and his family’s residence. We are counting on congress to step up in the coming months to pay back what it owes our city. This is a national responsibility and the burden cannot fall alone on our city and police department,” de Blasio said in a statement.

Negotiators did add nearly $6 billion extra money for the Pentagon and $4.3 billion more for the State Department to support the Obama Administration’s continued efforts to fight the terror group ISIS.

To help struggling states still recovering from Hurricane Matthew and floods in the Southeast, the legislation includes another $4 billion in disaster aid.

Bipartisan negotiators also agreed to provide $170 million to help Flint, Michigan, address the effects of contaminated water system that sickened residents over years.

The funding bill also sets aside over $800 million for a new federal effort to boost federal cancer research.

Mindful of voters’ low opinion of lawmakers in Washington, the legislation also blocks a scheduled pay increase for members of Congress.

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