A bishop has investigated the Muslim prayer service that took place in Church of England building in London and has pledged that no such service will take place again. The vicar, Canon Giles Goddard, today apologised for the "great consternation" and for "any offence" caused by the event.

The Bishop of Southwark, Christopher Chessun, had earlier asked the Bishop of Kingston, Richard Cheetham, to "investigate fully" the service at St John's Church Waterloo earlier this month.

"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 is quite clear that Islamic prayer should not take place in a consecrated building," said a spokesman for the Southwark diocese.

Today Bishop Chessun said: "The Bishop of Kingston has, at my request, now met with the Vicar of St John, Waterloo to discuss the Inclusive Mosque event which took place at St John, Waterloo on 6 March. Whilst it is very important to build good interfaith relations, it is clear that an act of worship from a non-Christian faith tradition is not permitted within a consecrated Church of England building.

"The Vicar has issued a statement expressing his sorrow at the offence this has caused and any infringement of Church of England guidelines. He has assured me of his intention to work within these guidelines in the future."

George Conger on the blog AnglicanInk described how the "jummah" had been held at St John's with the permission of Canon Goddard and organised by the Inclusive Mosque Initiative. The service was led by a woman imam and Canon Goddard read from Psalm 139: "Let us celebrate our shared traditions, by giving thanks to the God that we love, Allah."

Images and iconography of the Virgin Mary, Jesus and the stations of the cross were covered over during the event, which was videoed and appeared online. As a result of complaints, Canon Goddard met with Bishop Cheetham who is also Anglican president of the Christian Muslim Forum.

Canon Goddard said in a statement today: "The Inclusive Mosque Initiative event hosted by St John's Church, Waterloo, for International Women's Day has given rise to great consternation, and I am sorry for the offence caused and any infringement of Church of England's framework and guidelines.

"I am, by faith and tradition, a Christian. I stand by the Church of England's Declaration of Assent: The Church of England is part of the One, Holy, Catholic and Apostolic Church, worshipping the one true God, Father, Son and Holy Spirit. It professes the faith uniquely revealed in the Holy Scriptures and set forth in the catholic creeds, which faith the Church is called upon to proclaim afresh in each generation.

"Led by the Holy Spirit, it has borne witness to Christian truth in its historic formularies, the Thirty-nine Articles of Religion, The Book of Common Prayer and the Ordering of Bishops, Priests and Deacons."

He said it was in that context that he had tried to build a better understanding between faiths.

"The Church of England is in an especially responsible position as the established church, with a duty to try to engage with all the people of England. Now, more than ever, it is essential that we are able to meet in friendship across the boundaries of faith, and the event at St John's was part of attempts to enable that to happen. I remain committed to finding ways for Christians and Muslims to acknowledge our shared heritage and history, without minimising the uniqueness of both our traditions.

"I have assured the Bishop of Southwark of my commitment to work to build good interfaith relations, but to do so within the teaching and guidelines of the Church of England."

Dr Gerald Bray, director of research at the Latimer Trust at Oak Hill Theological College in London said on Facebook: "The simple truth is that Islam is the only major world religion that is explicitly anti-Christian. The Buddha, for example, could not have known anything about Jesus and did not develop his ideas in contrast to Christ. Muhammad, on the other hand, knew about Christians and Jews and could easily have become one or the other himself. Instead, he concocted his own religion based on elements of Judaism and Christianity and regarded it is the culmination (perfection) of both. You could say that Islam is related to Christianity in much the same way as Mormonism is, but this does not constitute 'a common tradition'."

Canon Andrew Stevens, of St Nicholas, Plumstead said Anglicans knew Jesus was "the unique and final revelation of God". Covering up the symbols of salvation, in order not to offend or to allow others to worship, was an act of "sacrilege" he added and it was especially an "affront" because it was done by a priest.

Fr Martin Hislop, of St Luke's, Kingston, said: "At a time when Christian men, women and children are being slaughtered in Iraq, Syria, Libya, Nigeria and elsewhere for their belief in the unique salvation delivered by Christ Crucified it is a scandal and an offence that a clergyman of the Church of England should embrace an act of islamic worship in a consecrated building dedicated to the glory of God, Father, Son and Holy Spirit."