The Bishop of Kingston has been called in by the diocese to investigate a Muslim service that was held at St John's Anglican church in Waterloo.
Last Saturday hundreds of Muslims packed the church in the event approved by the vicar, Revd Canon Giles Goddard.
The Telegraph newspaper reports that he invited the congregation to give thanks to "the God that we love, Allah".
He's said to have described the event as 'very moving' and that it was offering people a 'place to pray'.
It has been claimed that the service could have broken Church law which forbids any variation on services if it represents 'any departure from, the doctrine of the Church of England in any essential matter'.
In a statement the Diocese of Southwark said an investigation would now be launched.
"The Bishop of Southwark takes very seriously his responsibility to uphold the teaching of the Church and to work within its framework of legislation and guidance," it said.
"It is quite clear that Islamic prayer should not take place in a consecrated building.
"This is why he has asked the Bishop of Kingston to investigate fully what happened. It is inappropriate to seek to make further public comments on this matter until this has happened."
Watch video footage of the Muslim service: