The Justice Department is raising a red flag over an intelligence reauthorization bill passed by the Senate, raising fresh questions about the fate of the legislation.

“We appreciate the Senate’s reauthorization of three expired national security authorities. As amended, however, [it] would unacceptably degrade our ability to conduct surveillance of terrorists, spies and other national security threats," a Justice Department spokesperson said in a statement.  

The Senate voted 80-16 on Thursday to pass a bill that paired a reauthorization of three provisions of the USA Freedom Act, a 2015 intelligence reform bill, with some changes to the Foreign Intelligence Surveillance Act (FISA) Court. 

The bill initially passed the House in March as part of a deal negotiated by Attorney General William Barr and leadership in both parties. Majority Leader Mitch McConnell (R-Ky.) wanted to pass the House bill without changes.

But the Senate, during a two-day debate this week, made changes to the bill when they agreed to add an amendment from Sens. Mike Lee (R-Utah) and Patrick Leahy (D-Vt.) that would increase the role of outside legal experts in FISA court hearings, including allowing them to weigh in on some FBI surveillance requests.

Opponents of the legislation warned that it would bog down the FISA process, while supporters countered that it would be manageable because it would only apply to a small subset of people. 

The pushback from the Justice Department is only the latest sign that the intelligence bill could face hurdles to making it to the desk of President Trump, who has not said if he supports it.

Due to the Senate-made changes, the bill has to be passed by the House a second time. 

A House Democratic leadership aide told The Hill that the Senate bill would not be taken up on Friday when the chamber will take up a rules change to allow voting by proxy and a mammoth coronavirus relief bill.

"Democratic leadership assessing next steps," the aide added.

And there are already calls from progressives to make broader changes to the bill before it passes the House. 

The American Civil Liberties Union (ACLU) is calling on the House to revive an amendment from Sens. Ron Wyden (D-Ore.) and Steve Daines (R-Mont.) that would block law enforcement from being able to access web browsing data without a warrant.

The Senate narrowly failed to add the amendment to the bill during its debate. The amendment needed 60 votes to be added and got 59. Several senators who were expected to vote in favor, including Sen. Bernie Sanders (I-Vt.), were not present for the session.

Wyden in a tweet noted that "my amendment to secure browser history from warrantless spying would have passed with a full Senate present."

"Any renewal of government surveillance powers must have equally strong protections for Americans’ privacy," he added.