It was an "incredibly weak performance" by the Treasury secretary, Walker said. Representative Dave Brat of Virginia called Mnuchin's comments "intellectually insulting." Despite the grumbling, most Republicans voted for the deal.

To many Republicans, Trump's deal with Democrats showed that even with their party in control of the White House and both chambers of Congress, they can't easily accomplish their goals. They wanted spending cuts and a longer-term debt limit extension. House Speaker Paul Ryan of Wisconsin backed the bill after initially seeking a longer extension and then reversed course after Trump agreed to the short-term deal with Democratic leaders.

Republicans say Democrats may gain the upper hand in negotiations when the short-term agreements are due to expire in December. The agenda likely will include Trump's proposed border wall with Mexico, his decision to end a program that lets young undocumented immigrants stay in the U.S., and perhaps the debt limit.

Related: FEMA is almost out of money as Hurricane Irma threatens Florida

All of the votes against the bill were cast by Republicans. Many GOP members said they had little choice but to support the measure because funding is urgently needed for disaster relief.

"Of course I have to vote yes. It's my district that was hit," said Representative Blake Farenthold, whose Texas district includes Corpus Christi and much of the area along the Gulf of Mexico damaged by Hurricane Harvey. "The saving grace of this is we can revisit the debt ceiling in a couple of months and maybe get some spending reforms."

Replenish depleted FEMA disaster relief fund

With Hurricane Irma bearing down on Florida and tens of thousands suffering flood damage along the Gulf coast from Harvey, the bill will replenish the depleted Federal Emergency Management Agency disaster relief fund with $7.4 billion, plus $450 million in funding for the Small Business Administration and $7.4 billion for the Community Development Block Grant program to address housing needs in disaster zones.

The bill, H.R. 601, also extends the nation's flood insurance program to Dec. 8, a high priority in the wake of Harvey and Irma.

An earlier version of the bill containing just Harvey aid passed the House on a 419-3 vote Wednesday. Trump then surprised Republicans by agreeing to attach the short-term debt ceiling and government funding bill, even though the final bill doesn't include funding for a border wall. In May, Trump suggested a government shutdown in September would be needed to force Democrats to fund the wall on the U.S.-Mexico border. 

Bruising December

The legislation sets up a bruising December for Congress, which is already attempting to rewrite the U.S. tax code by the end of the year. December presents big opportunities for congressional Democrats and risks for Republicans.

Senate Minority Leader  Chuck Schumer of New York and House Minority Leader Nancy Pelosi of California had advocated for a short-term debt ceiling increase to obtain more leverage in December talks over a final spending deal for fiscal 2018. 

Democratic leaders, knowing their votes are needed to pass a debt ceiling increase, plan to seek higher domestic spending in those talks. They may use the occasion to push for legislation exempting undocumented immigrants who arrived in the U.S. as children from deportation.

Schumer said his hopes for an immigration deal have been raised by the "happy ending" that Trump provided to the September fiscal debate. Trump and Democrats also discussed working on a deal to end periodic debt ceiling votes, an idea that splits Republicans.

"For many years, people have been talking about getting rid of debt ceiling altogether," Trump told reporters Thursday at the White House. "And there are a lot of good reasons to do that, so certainly that's something that will be discussed.

Lost fight

Ryan and Senate Majority Leader Mitch McConnell of Kentucky lost the fight over the length of the debt ceiling extension at a tense Oval Office meeting Wednesday, hours after Ryan denounced a short-term debt extension in a press conference.

"The longer, the better for the stability of the credit markets. That's my strong opinion," Ryan said afterward. He added that in agreeing to the short-term extension, Trump "was interested in making sure that this is a bipartisan moment while we respond to these hurricanes."