"It was a request from the administration," Senate Appropriations Committee Chairman Richard Shelby, R-Ala., said Tuesday.
In 2017, the Trump administration scrapped a congressionally approved effort underway for several years to build a large campus for the bureau in Washington's suburbs, opting instead for a new headquarters on the site of the J. Edgar Hoover Building on Pennsylvania Avenue -- across the street from Trump's Washington, D.C., hotel.
The Justice Department inspector general is now investigating that decision, which Democrats say was an effort to protect the value of Trump's hotel by keeping the site across the street off the commercial real estate market, and prevent the construction of a competitor.
"They managed to have enough money for $2 billion dollars for the FBI headquarters that benefits Trump hotel and they say they have no money for food assistance?" said Senate Minority Leader Chuck Schumer, D-N.Y. "What the heck is going on?"
House Speaker Nancy Pelosi, D-Calif., said on Monday that the project is in the bill "so that the president -- nobody could build a hotel across the street."
Republicans, who are still divided on the details of the $1 trillion proposal -- which includes $1,200 direct payments to taxpayers, more funds for small businesses through the Paycheck Protection Program, liability protections for businesses and $100 billion to help schools and colleges reopen -- expressed confusion on Tuesday about the funding for the FBI headquarters in the proposal.
"That makes no sense to me," said Senate Judiciary Committee Chairman Lindsay Graham, R-S.C.
"I just don't get it," said Sen. Rick Scott, R-Fla.
"Even if the White House wanted it, I'd be against it because it's certainly not necessary," Sen. Mike Braun, R-Ind., said Tuesday.
"I am opposed to non-germane amendments," Senate Majority Leader Mitch McConnell, R-Ky., said on Tuesday after the Senate GOP weekly luncheon. "When we get to the end of the process I would hope that all of the non-COVID measures are out, no matter what bills they were in at the start."
McConnell was unaware on Monday that the provision made its way into the Senate GOP bill and told reporters to ask the Trump administration about it.
Arriving for a meeting with Republican senators on Tuesday, White House Chief of Staff Mark Meadows defended the FBI headquarters funding, telling reporters that "there are number of things in the last bill that had nothing to do with the coronavirus. I think everybody acknowledges that it's a funding mechanism.
"I don't see it standing in the way of us getting a deal," he added.
The General Services Administration referred questions about the status of the project to the FBI.
"The need for a new FBI headquarters facility has not abated. The FBI needs a building capable of meeting the increased demands of the nation's premier national security and law enforcement organization -- a facility that will enable and enhance the FBI's work for decades to come," an FBI official told ABC News. "The FBI will continue to coordinate with the General Services Administration, the Department of Justice, the Office of Management and Budget, and Congress on a path forward."
Trump last week defended efforts to fund the new FBI project in the coronavirus negotiations, along with his efforts to rebuild the bureau's headquarters at its current downtown location.
"They were looking in sites in Maryland and Virginia, in different places, but they would've been too far away. So I've been encouraging them to build it," he said.
Democrats on Tuesday also took aim at $30 billion in defense spending that Republicans included in their proposal, with Pelosi and Schumer calling it a "slush fund to defense contractors."
Shelby, the top GOP appropriator in the Senate, said the funding is important to support American jobs in the defense industry.
"A lot of it has been eroded right now, a lot of people off of work, a lot of suppliers involved in there," he said. "Every chance we get to build security for the country, that's important."
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