The Church of England's clergy have issued an extraordinary challenge to its conservative line on marriage by throwing out a bishops' report on sexuality.

In a major revolt against the CofE's hierarchy, members of the Church's General Synod rejected a report by top bishops that said there was 'little support' for changing the view that marriage was between one man and one woman.

The shock result plunges the Church into confusion on its stance on marriage with the bishops' report barred from being discussed until the end of this synod in 2020.

Although a majority of members voted in favour overall, a move by campaigners forced the synod to split into its three separate houses – the laity, the clergy and the bishops – with all three needing a majority for it to pass.

But the clergy voted by 100 to 93 against, in a rebuke to the bishops' authority.

It is unprecedented that a 'take note' motion, usually passed on the nod, should fail and highlights the tide of anger from all sides within the Church over the bishops' report.

Speaking in the debate the Archbishop of Canterbury, who met with rebels earlier on Wednesday, promised bishops 'will seek to do better' as he called for a 'remarkable' new teaching document on CofE's position on marriage.

'We are going to move on and find a radical new inclusion based in love, based in our Christian understanding careless neither of our theology nor ignorant of the world around us,' he said.

Jayne Ozanne, a gay member of the synod who led a campaign against the report, said she was 'thrilled'.

She said after the vote: 'We can now work together to help build a Church that is broad enough to accept the diversity of views that exist within it, courageous enough to address the deep divisions that exist between us and loving enough to accept each other as equal members of the Body of Christ.'

But Andrea Williams said the result should not be seen as a victory for LGBT activists. She was one of a handful of conservative members who voted against the report over concerns the report would lead to blessings for gay couples.

'What was clear from the debate was that the report tries to straddle positions that cannot be reconciled,' she said.

'Now what we need is clarity.

'We request the Church make clear the teaching on true marriage that is good for all and in line with the Church's apostolic teaching.'

Another synod member Susie Leafe, who leads the conservative grouping Reform, also voted against the report over concerns allowed for 'maximum freedom' for gay couples. She said it was time for the bishops to make a decision.

'We didn't get the clarification from the bishops that we asked for so therefore we voted against,' she told Christian Today.

The result is a major blow to the Archbishop of Canterbury's authority after he instigated three years of internal discussions costing more than £384,000 on talks designed to heal deep rifts within the Church of England.

The report was the result of those talks. It refused to budge on the Church's view on marriage but promised 'maximum freedom' within existing laws. It called for 'a fresh tone and culture of welcome and support' for LGBT people but did not go far enough for many liberal members.

Responding to the result the Bishop of Norwich, who led a reflection group behind the failed report, said he guaranteed the result would be listened to.

Another leading figure, the Bishop of Willesden, Pete Broadbent, warned of future conflicts.

'We will find this debate a continuing source of disagreement because we haven't coalesced around an end point,' he said.

'We don't yet know the next stage – nor yet when and whether we can bring any further report to synod.'