The Christian Institute and Christian Concern, as well as the former MP Ann Widdecombe have said the decision is unfair after the three major cinema chains refused to play a Church of England advert for the Lord's Prayer in December 2015.
Odeon, Vue and Cineworld said they have a policy of not showing political or religious advertisements, however buses have no such ban on religious advertising.
Buses in London, Manchester, Birmingham, Leicester and Bradford will carry the slogan 'Subhan Allah', meaning 'Glory be to God' in Arabic.
The advert's commissioned by the international aid charity Islamic Relief, before the festival of Ramadan where Muslims traditionally fast during daylight hours and give to charity.
Speaking to The Daily Mail Simon Calvert, from the Christian Institute, said he hoped these religious adverts were the start of a new era of "greater expressions of the Christian faith."
Referring to Vue, Odeon and Cineworld banning the Lord's Prayer at Christmas, he said: "People were surprised by the cinema advertising agenda to ban the Lord's Prayer, something we all grew up with.
"Audiences are capable of hearing expressions of Christian faith without running away screaming in horror."
Islamic Relief has said the posters will help raise money for victims of war and disaster in Islamic countries.
Director Imran Madden said: "There is a lot of negativity around Muslims.
"We want to change this perception of Islam.
"The campaign is about breaking down barriers and challenging misconceptions."
The bus company is unable to advertise a political party or political cause but has no rules on religious advertising.
