WASHINGTON — A dispute in Congress over whether to keep the Pentagon’s mandate that troops receive the coronavirus vaccine has stalled progress on the annual defense policy bill, with Republicans insisting on lifting the mandate and the Biden administration strongly resisting the move.

The bill, which authorizes a pay raise for American troops and is considered one of just a few pieces of must-pass legislation, perennially attracts a long list of proposals from lawmakers hoping to attach their pet project or policy.

This year, the $857 billion policy measure, which is set to increase the Pentagon’s budget by $45 billion over President Biden’s request, has become snarled by disputes over a host of unrelated issues. Top lawmakers have been haggling over legislation allowing cannabis companies to access banking institutions; a measure championed by Senator Joe Manchin III, Democrat of West Virginia, making it easier to build a natural gas pipeline in his state; and even an overhaul of the Electoral Count Act.

That has left congressional leaders to walk a precarious tightrope, balancing competing constituencies in the final weeks of the year and facing razor-thin majorities in both chambers.

“I will vote against my own bill,” if it becomes loaded with extraneous measures, declared Senator James M. Inhofe of Oklahoma, the retiring top Republican on the Armed Services Committee.

But the most heated point of contention appeared to be over the vaccine mandate, which has added a politically charged and highly emotional issue to the annual defense policy debate.

Republicans, especially Representative Kevin McCarthy of California, the minority leader who is campaigning for speaker, have made repealing the mandate one of their top priorities in the defense bill. They have long argued that the requirement amounted to federal overreach and eroded military readiness. Republicans said it continued to be a top concern that constituents have raised in calls and town hall meetings.

Mr. McCarthy said over the weekend that the defense bill would “not move” if it did not roll back the mandate, and some key Democrats have appeared open to scrapping the policy.

“I was a very strong supporter of the vaccine mandate when we did it,” Representative Adam Smith, Democrat of Washington and the chairman of the Armed Services Committee, told Politico, adding, “But at this point in time, does it make sense to have that policy from August 2021?”

Biden administration officials, including the secretary of defense, have said it is still very much needed, and are pushing back intensely on a repeal of the mandate.

“Vaccines are saving lives, including our men and women in uniform,” John F. Kirby, a spokesman for the National Security Council, said on Monday. “So this remains very, very much a health and readiness issue for the force.”

Service members are required to be vaccinated against a whole host of viruses. Starting in basic training, recruits receive shots protecting them from hepatitis A and B; the flu; measles, mumps and rubella; meningococcal disease; polio; tetanus, diphtheria and pertussis; and chickenpox in addition to Covid-19, according to the Defense Health Agency, which oversees health care for the armed forces.

Those sent overseas are required to receive additional vaccinations based on where they are sent and any special duties they may perform, such as shots to protect against anthrax, rabies, typhoid and yellow fever.

Across the armed services, a vast majority of service members are fully vaccinated against coronavirus, and nearly all are at least partially vaccinated, according to data released by the various branches.

The U.S. military has a history of vaccinating troops. It stretches back to Gen. George Washington requiring variolation, a type of inoculation, for his soldiers at Valley Forge in an effort to protect them against smallpox, according to Dr. John W. Sanders, a professor of medicine at Wake Forest University and an infectious disease specialist who served 23 years on active duty as a Navy doctor.

Calling the Covid vaccines “remarkably safe and effective,” Dr. Sanders said active duty personnel take vaccines that pose greater risks — such as for yellow fever, smallpox and measles, mumps and rubella — “and do not bat an eye.”

“Being appropriately trained, equipped and vaccinated is part of having a strong military, and if people are in uniform, they need to take these vaccines,” he said.

But Republicans have been increasingly outspoken about their opposition to the coronavirus vaccine mandate, pointing to the thousands of troops who were removed from service for refusing to comply.

“The Department of Defense Covid-19 vaccine mandate has ruined the livelihoods of men and women who have honorably served our country,” Senate Republicans wrote in a letter to their leaders last week. “While the Department of Defense certainly must make decisions that will bolster military readiness, the effects of the mandate are antithetical to readiness of our force, and the policy must be revoked.”

The debate is unfolding at a time when coronavirus mandates remain an intense point of contention, even after Mr. Biden declared in September that “the pandemic is over,” and as misinformation about the pandemic, particularly about vaccines, continues to spread, particularly on far-right platforms.

But it is only one of the issue holding up the defense measure. As time runs short for lawmakers to complete a hefty list of items in a lame-duck session, they have considered adding other measures to the defense bill, including a bipartisan measure to clarify the role of Congress and the vice president in counting electoral votes to confirm the results of presidential elections.

Democrats also are weighing whether to include the permitting proposal by Mr. Manchin, a centrist who demanded it over the summer as the price of his vote for the party’s signature climate, health and tax policy law.

The measure would ease the permitting process for wind, solar and fossil fuel infrastructure.

In the House, some liberals who oppose the construction of the gas pipeline in West Virginia have threatened to try to block the defense bill from being considered if Mr. Manchin’s permitting legislation is included.

“I respect him for trying to get what he wants, but I also believe that this is the will of the members, and we are responsive and responsible to our communities,” Representative Pramila Jayapal, Democrat of Washington and the chairwoman of the Congressional Progressive Caucus, said.

Senate Republicans, still bitter over the deal Mr. Manchin brokered that paved the passage of the climate, health and tax policy law, have signaled they would also reject the measure.

A bipartisan group of senators also is pushing to include a measure to bar federal banking regulators from taking action against banks that serve cannabis businesses operating legally under state law.

“I think there’s about 75 to 80 votes in favor,” said Senator Rand Paul, Republican of Kentucky, and one of the bill’s supporters. “Instead of people walking around with bags of $100,000 of cash, they’ll put it in a legitimate bank; they’re more likely to pay their taxes, they’re more likely to be law-abiding citizens.”

David McCabe and Emily Cochrane contributed reporting.

Catie Edmondson and John Ismay

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