WASHINGTON — Congress limped Wednesday toward a rare bipartisan agreement on a $1.1 trillion spending bill to keep most of the government operating through next year, but dysfunction once again threatened to derail it.

The fissures emerged as lawmakers in both parties balked over details in the 1,600-page bill, including one provision that rolled back Wall Street regulations and could deliver a financial bounty to big banks, and another that would allow big donors to wield even more influence over political parties. More conservative Republicans continued to argue that the bill also did not do enough to try to scale back President Obama’s executive action on immigration.

Even with the resistance, Republican leaders and some Democrats expressed confidence that a government shutdown would be averted. Senator Barbara A. Mikulski, Democrat of Maryland, who as the chairwoman of the Senate Appropriations Committee helped to negotiate a deal, called the spending plan a “monumental achievement” in an era of seemingly intractable partisan divides.

The objections mean that Congress will probably need to pass a short-term funding measure to keep government operations running beyond Thursday — the current deadline — while the final disputes are sorted out, even as Republicans expressed confidence that the spending agreement would ultimately be approved.