The Anglican Bishop of London, the Rt Rev Sarah Mullally, said churches might not return to normal services before the end of the year.
Mosques, churches and temples in the UK have been closed for almost two months.
The prime minister is due to make a statement about the lockdown restrictions later.
It is not clear if the government will change its guidance for places of worship.
But senior religious leaders have told the BBC that faith communities will have to endure long-term changes to their worship in order to prevent the spread of coronavirus.
Ibrahim Mogra, a senior imam in Leicester, warned the prime minister not to ease restrictions on places of worship before the end of Ramadan, the Islamic holy month.
"I am not convinced that we can maintain social distance," he said.
"Within a mosque set up the first thing is the removal of footwear. And then it's the ritual washing, and then going into the main prayer hall," he said.
"We are talking about a five times regular daily attendance compared to other places of worship," he said. "So we are talking about really large numbers of people."
The Muslim Council of Britain, the UK's largest Muslim umbrella organisation, is consulting its members before issuing guidance this weekend for mosques that are considering reopening.
"The majority of the mosques that we have consulted are of the view that they do not wish to open during Ramadan," Mr Mogra said.
"We do not want to be the ones who cause harm to others."
The Rt Rev Sarah Mullally, the Bishop of London, is leading the Church of England's planning for reopening its buildings. She said there would have to be significant changes to key aspects of Christian worship "for some time" to come.
"I don't envisage, even up to the end of the year, we will be back to our normal services.
"We'll have some churches doing things differently. And of course, this approach will depend on the part of the country you are in. Being in Devon is very different to being in the centre of London. So we need to approach this based on our local circumstances," she said.
"There are some very challenging questions that we'll have to face, not least about singing and about the receiving of Holy Communion. So the future will look different.
"But we want to continue to support people in their spiritual journey with their faith," she told the BBC.
"When we open our church buildings, we will still have to ensure physical distancing. We'll have to make sure people can wash their hands on the way in and on the way out. We are likely not to be able to use hymn books or service sheets or sing."
Many religious communities have seen a spike in numbers as services and prayers are forced online during the pandemic.
A survey by ComRes last week found that almost one in four British adults have watched or listened to a religious service since lockdown began. Academics from British Religion in Numbers estimate that typically just 6% of adults regularly attend a religious service.
Bishop Sarah Mullally said the findings showed that while religious buildings are closed "the Church continues to be open".
She added: "Now there is going to be a challenge for us in the future, about asking ourselves why do more people access online than may be coming to our buildings? How do we enable them to enter into our community, to be part of our community in church?"
Imam Ibrahim Mogra said the Islamic festival of Eid, which ends the month long fast in Ramadan, would not feel the same.
"As an imam when I finish with the Eid prayers, hundreds upon hundreds queue up to hug me," he said.
"There are friends I know who wait all year long to greet me and to hug me on that special day of Eid," he added.
"So we will dearly miss all this. But we must understand that we have a duty to protect others and to protect ourselves. Our celebrations may be dampened. But if we remain disciplined as we have so far, I think the next year we can make up for it and have a really big party."
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