All places of worship in Switzerland with more than 50 people attending services or events are now required to control access by asking attendants to show a Covid passport.
It comes as part of a set of restrictions introduced by Swiss authorities which seek "to prevent hospitals from being overstretched".
The country has the highest incident rate in Europe, after the UK, registering 402 infections per 100,000 residents over the past 14 days.
All of those over 16 will be required to show an official certificate of vaccination, proof of having recently recovered from the virus or proof of a negative test.
Access to indoors spaces such as bars, restaurants and museums will also be subject to having a Covid certificate.
The Association of Free Churches in Switzerland disagrees with the measure saying that they have "encouraged people to get vaccinated" but want to respect people's personal decisions.
"Visiting a church service is something elemental for Christians. It is an individual but also communitarian and spiritual experience".
While the association agrees the measure will bring a sense of "security" to people, it argues that it affects the "personal decisions" of citizens.
"Worship services are an expression of the free practice of religion and must not be regulated by identity checks of any kind."
Both the mainline Protestant Reformed Church and the Roman Catholic Church have supported the new restrictions.
Those who fail to comply with the rules risk a fine of €92 (£72). The measure is expected to remain in place until 24th January 2022.