Conference negotiators voted to eliminate the proposed tax and adopted a new plan to pay the projected five-year, $20 billion cost of the legislation.
The new plan would bring an early end to the Troubled Asset Relief Program, the mammoth financial system bailout effort enacted in 2008, and redirect about $11 billion toward heightened regulation of the financial industry.
The conferees also voted to increase the reserve ratio of the Federal Deposit Insurance Corporation, but specified that small depository institutions — those with less than $10 billion in consolidated assets — be exempt from paying any increase.
They also voted to permanently set the maximum deposit insured by the F.D.I.C. at $250,000 per account, a change that would further raise the amount banks must pay toward the coverage.
The votes were again on party lines, with Democrats in favor and Republicans opposed. Senate negotiators voted 7 to 5 to approve the revised package, and House negotiators voted 20 to 11.
Democrats expressed frustration, saying they were adjusting the bill to meet the demands of centrist Senate Republicans only to face stiff criticism from Republicans on the committee.
“Frankly, I’m caught in the middle of an intra-Republican debate here,” said Representative Barney Frank, Democrat of Massachusetts and chairman of the Financial Services Committee, who presided over the conference proceedings with Senator Christopher J. Dodd, Democrat of Connecticut and chairman of the banking committee.
The need to reopen negotiations was slightly embarrassing for Democrats and represented a price they had paid for rushing to complete the legislation.
President Obama had requested that the package be completed by the end of last week so that it could be sent to his desk before Congress went home for the Fourth of July. The proposed tax on banks was one of the provisions included as Democrats completed the bill shortly before daybreak on Friday.
But the Democrats were forced to change the bill after Senator Scott Brown, the Massachusetts Republican who had supported the Senate bill, said he would oppose the final version because it contained the tax on banks. Other senators who had supported the original Senate version also said they were unhappy with the levy on financial institutions.
Senate Democrats cannot advance the measure without the cooperation of at least some Republicans, and the death on Monday of Senator Robert C. Byrd, Democrat of West Virginia, who had supported the bill, further complicated the legislative math.
With the changes, Democrats said they were confident they would be able to muster the needed votes in the Senate, at least on the procedural motion to end debate. The vote on final adoption of the conference report requires only a simple majority.
But some Republicans who oppose the larger financial regulation bill reacted furiously to the idea of using spending authority freed up by ending the Troubled Asset Relief Program before its scheduled Oct. 3 expiration.
Senator Judd Gregg, Republican of New Hampshire and a member of the conference committee, noted that the asset relief program money was borrowed in the first place.
Mr. Gregg called the plan “pure deception” of taxpayers, who he said were promised that any money left from the program would be paid back to the Treasury. “I know this because I wrote it,” he said. “As this money comes back, we shouldn’t spend it.”
Mr. Frank said the full House could vote on the adjusted final bill as soon as Wednesday. But given procedural hurdles it seemed unlikely that the Senate could approve the measure before the holiday recess.
The Obama administration supported the change in the final bill, in part because of concern that the proposed fee on big banks in the financial regulatory measure would complicate Mr. Obama’s efforts to impose a separate, larger $90 billion bank tax over 10 years.
Mr. Brown was one of four Republicans to support the Senate version of the financial regulatory bill, which did not include the fee on banks and hedge funds. And he said he was frustrated that it was added to the bill by the conference committee.
In a letter sent Monday to Mr. Dodd and Mr. Frank, Mr. Brown wrote: “If the final version of this bill contains these higher taxes, I will not support it.”
Senator Olympia J. Snowe, Republican of Maine, who also supported the Senate version, made the same complaint on Monday but said she had not decided if it was reason to switch her vote.
Mr. Brown’s opposition to the bank fee may put him in an awkward position given that there were few popular options to pay for the legislation.
Democrats had argued that the fee on big banks and hedge funds meant that the wealthiest players on Wall Street would bear responsibility for the new regulatory environment necessitated by the past mistakes of financial institutions.
Mr. Brown, in his letter, complained that a tax on banks would be passed along to consumers. But using money from the Troubled Asset Relief Program opens him to criticism that he forced taxpayers to pick up the tab.
Heather Booth, director of Americans for Financial Reform, said she believed Mr. Brown’s reasons for opposing the bank fees missed the point of overhauling the regulatory system.
“Not passing this bill will cost taxpayers more,” Ms. Booth said. “It increases the risk in the economy over all.”
She said her organization believed the biggest banks — approximately 30 with assets of more than $50 billion that would be subject to the assessments — had fanned the opposition.
Senate Democrats need 60 votes to close debate on the conference report and move to a final vote. There are now 58 senators in the Democratic caucus, including two independents.
One Democrat, Senator Russ Feingold of Wisconsin, has said he will oppose the regulatory overhaul because he does not believe the bill is tough enough.
Senator Maria Cantwell, Democrat of Washington, who also opposed the bill, has not said how she will vote, but she could agree to help Democrats overcome a Republican filibuster by supplying the 60th vote on procedural grounds but then oppose the final measure.