The US Senate was expected on Tuesday to hold a key procedural vote on a funding bill to avert a federal government shutdown, after a tense standoff over a controversial energy-permitting provision proposed by the West Virginia senator Joe Manchin ended with its withdrawal.

After the permitting provision drew opposition from both parties, Manchin said he had asked that it be withdrawn.

In a statement late on Tuesday afternoon, the Democrat said: “It is unfortunate that members of the United States Senate are allowing politics to put the energy security of our nation at risk.

“The last several months, we have seen first-hand the destruction that is possible as Vladimir Putin continues to weaponize energy. A failed vote on something as critical as comprehensive permitting reform only serves to embolden leaders like Putin who wish to see America fail.

“For that reason and my firmly held belief that we should never come to the brink of a government shutdown over politics, I have asked Majority Leader [Chuck] Schumer to remove the permitting language from the continuing resolution we will vote on this evening.”

The measure was sharply criticized by progressives led by Bernie Sanders, the Vermont independent, and was struggling to gain support among Republicans, even those who have long championed permitting reform.

Without action, government funding will run out at midnight on Friday. If Congress fails to pass a bill by then, it would cause a messy shutdown. With Democrats in control of both chambers, that could generate what many believe would be an avoidable headache just weeks before the crucial midterm elections.

Before he withdrew his proposal, Manchin argued in a Wall Street Journal opinion piece that it would enact “common-sense permitting reforms” and “help secure America’s energy future”.

But Sanders had already said he would vote against any measure that included Manchin’s proposal, which critics say would gut clean water and environmental protections.

In a tweet, Sanders lashed out at the senators and editorial boards supporting the plan. He said: “I do believe the future of the planet is more important than the short-term profits of the fossil fuel industry. Defeat the Big Oil side deal.”

The proposal was part of a deal between Manchin and Schumer to secure Manchin’s vote for Joe Biden’s landmark healthcare and climate legislation, the Inflation Reduction Act (IRA).

After more than a year of negotiations, Manchin agreed to give his necessary 50th vote to the plan, which made good on long-sought Democratic policy ambitions and is credited with boosting morale among the party’s base ahead of the midterm vote.

With that bill signed into law, however, Schumer struggled to find 60 votes for Manchin’s permitting reform. Several Senate Democrats argued that the move would undermine the climate proposals in the IRA, which were already greatly scaled back to appease Manchin.

The permitting provision would have fast-tracked the process for energy infrastructure, including large fossil fuel projects critics say will undermine climate goals. It would also make it easier for the Mountain Valley pipeline to proceed, a top priority for Manchin long delayed by environmental violations and judicial rulings.

When progressives learned of Manchin’s proposal, they revolted. In a letter to colleagues last week, Sanders implored Democrats not to support the “disastrous side deal” that he warned would “make it easier for the fossil fuel industry to destroy the planet and pollute the environment”.

The choice before Congress was clear, Sanders wrote. “We can listen to the fossil fuel industry and climate deniers who are spending huge amounts of money on lobbying and campaign contributions to pass this side deal. Or we can listen to the scientists and the environmental community who are telling us loudly and clearly to reject it.”

Tim Kaine, a Democrat of Virginia, also said he would vote against the permitting reform. Kaine said he was not consulted on the potential impact of greenlighting the Mountain Valley Pipeline, which would run through his state.

Other top Democrats said keeping the government running was the bigger priority.

“I am disappointed that unrelated permitting reform was attached to this bill. This is a controversial matter that should be debated on its own merits,” said Patrick Leahy, the chairman of the appropriations committee. “However, with four days left in the fiscal year, we cannot risk a government shutdown; we must work to advance this bill.”

The proposal also divided Republicans. Though the GOP has long pushed for permitting reform, the minority leader, Mitch McConnell, urged his caucus to oppose Manchin’s proposal. Most of the chamber’s 50 Republicans, still smarting from Manchin’s change of heart on the IRA, appeared poised to vote against the measure.

In an interview with Fox News on Monday, Manchin said he anticipated opposition from Sanders and “extreme far-left” Democrats, but not from Republicans.

“What I didn’t expect is that Mitch McConnell and my Republican friends would be stacking up with Bernie or trying to get the same outcome by not passing permitting reform,” he said.

Manchin’s proposal was attached to a stopgap measure that would fund the federal government through 16 December, thereby allowing negotiations to resume after the November vote. Included in the funding bill are billions of dollars in support for Ukraine; an extension of a Federal Drug Administration user fee program that was set to expire; relief funds for the water crisis in Jackson, Mississippi; money for resettling Afghan migrants; and assistance to help families afford rising energy costs.

Schumer was expected to strip Manchin’s proposal from the bill if necessary. Manchin insisted he was “optimistic” about the bill’s chances, and expected to win support from most Democrats and enough Republican votes to secure its passage.

But then came his statement on Tuesday.

“We should never depend on other countries to supply the energy we need when we can produce it here at home,” he said, adding: “Inaction is not a strategy for energy independence and security.”