Millions of people across the world tuned into online church services on Sunday as their usual places of worship were closed, but in some places clerics insisted on their doors remaining open.

The day after Pope Francis delivered a blessing in an empty St Peter’s Square, watched on television by an estimated 11 million people, Sunday services were held at some of Russia’s largest religious sites after Orthodox church leaders said they were an expression of religious freedom.

Dozens of parishioners, many of them elderly, crowded into Kazan Cathedral in St Petersburg to receive communion. Earlier this month, the cathedral came under fire for continuing to exhibit a relic of John the Baptist despite fears that visitors kissing the exhibit could hasten the spread of coronavirus.

In virus-hit Louisiana, hundreds of worshippers attended services on Sunday, flouting a ban on large gatherings. An estimated 500 people of all ages filed inside the Life Tabernacle church in Central, a city of nearly 29,000 outside Baton Rouge

The Russian Orthodox church had insisted that mayors could not close churches and that it would continue to “fulfil its pastoral duty” unless given an order from the Kremlin.

But later on Sunday the church’s leader, Patriarch Kirill of Moscow, called on believers to refrain from visiting churches.

The liturgy in Kazan Cathedral, St Petersburg, on Sunday. Photograph: Peter Kovalev/Tass

Speaking after the liturgy at Christ the Saviour church in Moscow, Kirill said: “I have been preaching for 51 years, calling on people to come to church, overcome the gravitation of their own ill will and external circumstances, I dedicated my entire life to this call and I hope you understand how difficult it is for me to say now: refrain from visiting churches.”

In Romania and Georgia, two countries with strongly Orthodox Christian populations, there has been consternation over the insistence of some priests on continuing to use a shared spoon for the communion ritual.

Last Sunday, the day after Romania had been put into a strict lockdown, footage emerged from the city of Cluj of priests using a shared spoon. In Georgia, while the church has told worshippers not to spend long periods of time in churches and not to come if ill, it has rejected calls to abandon the reusing of spoons, claiming that as communion is a holy ceremony it is not possible to get ill during it.

In devoutly Catholic Poland, coronavirus restrictions limited the number of churchgoers to 50 at a time, and this was reduced again last week to five. Archbishop Stanisław Gądecki, the head of the Polish episcopate, earlier in March called for more church services to accommodate worshippers, as not praying during the epidemic would be “unthinkable”. However, he has since urged faithful to use media broadcasts of services to prayer, especially over the Easter period.

In Brazil, the president, Jair Bolsonaro – who has called the coronavirus a “little flu” and attacked lockdown – included churches in a list of “public services and essential activities” essential for the “survival, health and safety” of the population, provided they followed health ministry guidelines.

Two days after Bolsonaro’s pronouncement, a judge in Rio de Janeiro state suspended his decree. Cathedrals in São Paulo and Rio de Janeiro are now closed. And while some churches are still open for prayer, mass and services have mostly moved online.

Dom Walmor Azevedo, the archbishop of Belo Horizonte and president of the National Conference of Bishops of Brazil (CNBB), last week told congregations to “stay at home”. The CNBB and other Catholic organisations called Bolsonaro’s “disinformation campaign” a “serious threat to all Brazilians”.

About half of Brazilians are Catholic, but a growing number – currently 31% – belong to evangelical churches, which largely support Bolsonaro. Brazil’s biggest, the Universal Church of the Kingdom of God, said on Thursday that where services are not allowed, its churches are open for prayer. Where services are allowed, it controls numbers entering and provides soap and water.

Rio’s Assembly of God Victory in Christ church is open every day for “prayers and to attend those who need it”, said its pastor, Alexandre Camargo, but services went online even after it won a court battle to stay open. Rio’s Attitude Baptist church – frequented by Brazil’s first lady, Michelle Bolsonaro – is only holding online services.

“People are really suffering with this, because they need this spiritual, emotional and financial support,” said Pastor Josué Valandro Jr. “It is very serious to close all the churches.”

The Vatican said at the weekend that Pope Francis did not have coronavirus after testing of Holy See staff resulted in one new case. The total number of people with Covid-19 at the Vatican is now six. “I can confirm that neither the Holy Father nor his closest collaborators are involved,” a spokesperson said.

• This article’s headline and subheading were amended on 1 April 2020 to better reflect the text.