The Friday vote for flood assistance would be followed by another vote Jan. 15, the first full legislative day of the new Congress in the House, on an additional $51 billion, Boehner said.
"Getting critical aid to the victims of Hurricane Sandy should be the first priority in the new Congress," the Ohio Republican said in a statement he released with Majority Leader Eric Cantor, R-Va. "That was reaffirmed today with members of the New York and New Jersey delegations."
His decision followed an explosion of criticism from enraged Northeastern lawmakers and governors from both parties after he first said he would hold off on the vote until after the new Congress was sworn in Thursday -- which The Wall Street Journal said could have pushed the vote into late January or February.
"There is only one group to blame for the continued suffering of these innocent victims," Republican New Jersey Gov. Chris Christie said in a news conference Wednesday. "The House majority and their speaker, John Boehner."
"Shame on you! Shame on Congress," Christie said. "Put aside the politics and help our people now."
Christie, widely seen as a potential 2016 presidential contender, said Boehner had refused to take his calls Tuesday night.
After finally getting through Wednesday morning, Christie said he didn't trust Boehner to deliver.
"I'm not going to get into the specifics of what I discussed with John Boehner today," he told reporters in New Jersey. "But what I will tell you is there is no reason at the moment for me to believe anything they tell me. Because they have been telling me stuff for weeks, and they didn't deliver."
He accused the House leadership of duplicity and selfishness, saying the inaction "is why the American people hate Congress."
Rep. Peter King, R-N.Y., said Boehner's initial move betrayed the people of New York and New Jersey. He said local GOP campaign donors would now be "crazy" to donate to the party.
He called Boehner's initial decision a "cruel knife in the back" to his region.
Rep. Michael Grimm, R-N.Y., whose Staten Island district was among the hardest hit, threatened not to vote for Boehner in the election for speaker this week.
The aid package had drawn opposition from Republicans outside the Northeast who called it bloated and without proper oversight.
The money is supposed to rebuild mass transit, repair housing and replenish Federal Emergency Management Agency funds used to help Sandy victims.
Many Democrats and Northeastern lawmakers from both parties said the aid was desperately needed and in line with Congress's response to previous natural disasters.
Earlier aid packages were passed within a few weeks of the incidents. Sandy hit the Northeast Oct. 29, with particularly severe damage in New Jersey and New York.
U.S. damage is estimated to top $63 billion.
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