Dozens of Muslims took part in the "Inclusive Mosque" event at St John's Church in Waterloo in a prayer service within the Church of England premises.
Reverend Canon Giles Goddard, a prominent liberal cleric who joined in the event, read a passage from the Bible and invited the congregation to give thanks to "the God that we love, Allah".
Goddard, described the service, last weekend, as "very moving" and said it was simply an expression of the church's desire to offer people a "place to pray", the Daily Telegraph reported.
They said the service marked a breach with canon law which forbids any variation from the official liturgy if it contains "any departure from, the doctrine of the Church of England in any essential matter".
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Goddard explained the Inclusive Mosque Initiative, a group that allows both women and men to lead worship, approached him to host the event to mark International Women's Day on March 8.
"I said 'yes, of course, come' not realising that this would be controversial. We are offering a place for people to pray so it made absolutely perfect sense. We should be offering places to pray, we are the Church of England," he said.