The must-pass continuing resolution, or CR, which would keep federal agencies operating from Saturday through Dec. 9, received only 45 of the 60 votes needed to limit debate and be considered for passage by the 100-seat Republican-controlled Senate.

Forty Democrats and two independents opposed the CR because it lacked a $220 million aid package to address the drinking-water crisis in Flint, Michigan. It also drew opposition from 13 Republicans, including Senator Ted Cruz, the former presidential candidate.

Senate leaders said they would explore alternatives to avoid a shutdown.

Without an extension, many federal agencies will run out of operating funds when the government fiscal year expires at midnight on Friday.

The bill includes $1.1 billion to combat the Zika virus and $500 million for flood relief in Louisiana and other states.

"This is a 10-week funding bill. Its contents command broad support. It contains zero controversial riders," Senate Majority Leader Mitch McConnell said before the vote.