The St Nicholas Cathedral in Vienna's Landstraße district said on Thursday that a pokemon monster called Raa666 appeared the middle of the orthodox sanctuary in the game.
In their complaint to the company operating the game Niantic Labs Inc, the church requested that the pokemon be immediately and permanently removed.
In the letter, they said the church is “a sacred building and as such should exclusively be used for worshipping purposes”.
It is not the first time the augmented reality app has come under fire in Austria for its choice of locations for pokemon hunting or battles.
The head priest of Stephansdom in Vienna's city centre, Toni Faber, said that Pokemon Go are not welcome in the church. “It is not suitable to place Pokemon in the church,” he told Österreich newspaper.
The response of church officials in Austria differs from that of many churches in other countries, which have welcomed Pokemon Go players, seeing the game as an opportunity to boost numbers.
It is thought churches have become key stops in the game due to their size.
One church in the UK encouraged players to come back for Sunday mass and put up a sign that read: “Join us for a cup of tea after the service at 12.14. Jesus cares about Pokemon gamers.”
Churches in the United States have also been advertising themselves as Pokestops with the hope of attracting new members.
Pokemon battles on Nazi memorial
There was also anger in Graz after it was revealed a memorial to victims of Nazism in the city's central cemetery was used as a location for Pokemon battles.
The fact that players can play in Pokemon battles right next to the memorial dedicated to the many thousands of people who died as a result of Nazi persecution was described as ‘intolerable' by a spokesperson for local mayor Siegfried Nagl (ÖVP).