The provision would further block the transition of the program from the CIA to the Pentagon.
Senate Majority Leader Harry Reid (D-Nev.) late Wednesday set up a procedural vote on the $1 trillion omnibus spending bill, a move that should let the Senate pass it by Saturday.
The House voted Wednesday to advance a $1 trillion bill funding the government.
The Senate voted 86-14 for a bill that keeps the government funded through Saturday.
The continuing resolution would keep the government running through Saturday.
House Agriculture Committee Ranking Member Collin Peterson (D-Minn.) said Tuesday he is open to considering a farm bill dairy compromise that Chairman Frank Lucas (R-Okla.) is working on.
A debate about funding for public transit systems roiled an otherwise largely congenial House hearing on Tuesday about the future of transportation funding.
At issue was the approximately 2.8 cents per gallon of the 18.4 cents per gallon federal gas tax is set aside for public transit.
Heritage Action and the Club for Growth encouraged Congress to vote against spending bill.
House Transportation Committee Chairman Rep. Bill Shuster (R-Pa.) said on Tuesday that he wants the House to pass a new transportation funding bill by August to allow time for conference negotiations with the Senate.
The current transportation funding bill, which is a $109 billion measure that was passed in 2012, expires in September.
“My hope is to get reauthorization done on time,” Shuster said. “We hope to take committee action in the late spring or early summer with the goal to be on the House floor before the August recess. This way there will be time to conference our bill with the Senate’s bill.”