The weekly rhythms of Catholic life have started to return at Our Lady of Lourdes in Harlem. The pews are packed on Sunday mornings, prayer groups meet after work and the collection plate is almost as full as it was before the coronavirus pandemic began.

But parishioners are starting to worry about the virus again.

“For a little while everyone felt more free, not using masks and things like that,” said the Rev. Gilberto Ángel-Neri, the pastor. “But now that we hear all the news about the Delta variant, everyone is using masks again.”

The progress made at Father Ángel-Neri’s church, and at houses of worship across New York City, may be threatened by a rise in virus cases in the past month and by an uneven patchwork of rules governing vaccination that can differ from one place to another.

New rules that have been enacted in recent weeks to curb the spread of the virus’s more contagious Delta variant require New Yorkers to show proof of vaccination to participate in many indoor activities, including sitting inside restaurants or bars, going to a gym or nightclub and visiting a museum or zoo. But they do not apply religious services.

“Faith is a light to help you navigate through uncertainty and darkness, but what a lot of people have been grappling with is what do you do when church itself becomes a place of anxiety,” said John Gehring, the Catholic program director at the advocacy group Faith in Public Life.

Religious leaders, he said, “want people to come back to church but to do that safely is a hard thing to do in an environment where there are so many unknowns.”

Houses of worship have struggled over the past year as pandemic-related rules forced them to shut their doors for months and then limited how many people were allowed inside at a time. Most depend on donations to pay their bills, and while the number of worshipers and the size of their donations has slowly begun to rebound, the progress remains tenuous.

Most churches in the city do not require worshipers to be vaccinated.

Instead, rules vary from place to place. For example, vaccination is required to visit the campus of Fordham University, a Jesuit school, but not to enter the Catholic church around the corner.

Many Reform Jewish temples, including Central Synagogue in Manhattan and the Brooklyn Heights Synagogue, either require vaccination or plan to to do so by the High Holy Days next month, community leaders said.

Avi Shafran, a spokesman for Agudath Israel, an Orthodox Jewish umbrella group that sued New York last year over the state’s coronavirus restrictions, said that Orthodox leaders did not want the government to impose a mandate.

Community leaders, Mr. Shafran said, do “not want those who, for whatever reason, are unvaccinated to be faced with a draconian regulation that limits their participation in religious life.”

The leaders of individual Orthodox synagogues were “considering” requiring vaccinations based on the situation in their communities, he said, although he could not name any.

Catholic leaders have declined to answer questions about why they do not require worshipers to show proof of vaccination.

In November, the Roman Catholic Diocese of Brooklyn won a Supreme Court case against Gov. Andrew M. Cuomo that overturned public health restrictions on houses of worship. Since then, neither the city nor the state has moved to impose any new restrictions.

“We do not view religious worship as ‘indoor entertainment,’” said Bill Neidhardt, a spokesman for Mayor Bill de Blasio. “Right now, our approach is to continue partnering with faith leaders to promote the vaccine, deploy mobile vaccine vans to houses of worship and recruit religious organizations to take advantage of the vaccine referral bonus.”

Mr. Neidhardt declined to say whether concerns about religious freedom, or the example of the Supreme Court decision last fall, had influenced the city’s policy. But many religious leaders and analysts see a connection.

“Of course it doesn’t apply to houses of worship, as the governor learned last year,” said Rabbi Serge Lippe of Brooklyn Heights Synagogue. But he said religious institutions should follow the same rules as secular institutions.

“We are not looking for exemptions from common sense health guidelines, we want to follow common sense health guidelines,” he said.

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David Gibson, the director of the Center on Religion and Culture at Fordham University, said that when it comes to requiring vaccines, “everyone is trying to avoid this issue.”

Many parish leaders said they had their hands full rebuilding their congregations after the upheaval of the past year and a half.

When the pandemic forced Our Lady of Lourdes to close, parishioners lost a vital community center, Father Ángel-Neri said. The parish also lost about $3,000 a week in donations.

Today, he said, the crowds at Mass are smaller than before the pandemic, but those who come “want to be here and they want the parish to succeed.”

That view was shared by the dozen or so people who came to a Spanish-language Mass in the church’s brightly lit basement chapel one night last week.

“What we get from being here is so much more important than being scared,” said Ana Sanchez, 48. “It helps us get through these hard times. My faith is more important than anything, even the pandemic.”

“We are the in presence of God the Father, and that’s the important thing,” said Melania de Jesus, 51.

Understand Vaccine and Mask Mandates in the U.S.

• • Vaccine rules. On Aug. 23, the Food and Drug Administration granted full approval to Pfizer-BioNTech’s coronavirus vaccine for people 16 and up, paving the way for an increase in mandates in both the public and private sectors. Private companies have been increasingly mandating vaccines for employees. Such mandates are legally allowed and have been upheld in court challenges.
  • Mask rules. The Centers for Disease Control and Prevention in July recommended that all Americans, regardless of vaccination status, wear masks in indoor public places within areas experiencing outbreaks, a reversal of the guidance it offered in May. See where the C.D.C. guidance would apply, and where states have instituted their own mask policies. The battle over masks has become contentious in some states, with some local leaders defying state bans.
  • College and universities. More than 400 colleges and universities are requiring students to be vaccinated against Covid-19. Almost all are in states that voted for President Biden.
  • Schools. Both California and New York City have introduced vaccine mandates for education staff. A survey released in August found that many American parents of school-age children are opposed to mandated vaccines for students, but were more supportive of mask mandates for students, teachers and staff members who do not have their shots.  
  • Hospitals and medical centers. Many hospitals and major health systems are requiring employees to get a Covid-19 vaccine, citing rising caseloads fueled by the Delta variant and stubbornly low vaccination rates in their communities, even within their work force.
  • New York City. Proof of vaccination is required of workers and customers for indoor dining, gyms, performances and other indoor situations, although enforcement does not begin until Sept. 13. Teachers and other education workers in the city’s vast school system will need to have at least one vaccine dose by Sept. 27, without the option of weekly testing. City hospital workers must also get a vaccine or be subjected to weekly testing. Similar rules are in place for New York State employees.
  • At the federal level. The Pentagon announced that it would seek to make coronavirus vaccinations mandatory for the country’s 1.3 million active-duty troops “no later” than the middle of September. President Biden announced that all civilian federal employees would have to be vaccinated against the coronavirus or submit to regular testing, social distancing, mask requirements and restrictions on most travel.

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