The boss of the charity that runs two Southampton secondary schools has called on the church to re-examine its attitude towards homosexuals.
Leading, evangelical minister The Rev Steve Chalke says it gives a negative attitudes which can have a negative impact on people's mental and physical health.
Mr Chalke founded the Christian charity Oasis, said he had become increasingly aware of the suffering of homosexual people within the church.
The organisation has run the 950-pupil Oasis Academy Lordshill and the 1,150 pupil Oasis Scademy Mayfield, both in Southampton, since 2008.
Mr Chalke has now called for further debate on same-sex relationships, and has launched an online support service to offer help to gay people who have been hurt by practices and teachings of some parts of the church.
In an article for Christianity Magazine, Mr Chalke, who is senior minister of Oasis Church Waterloo in London, speaks of the conflict between his understanding of ''the principles of justice, reconciliation and inclusion (that) sit at the very heart of Jesus' message'', and the Bible's teaching ''that the practice of homosexuality, in any circumstance, is a sin or 'less than God's best'.''
In the article, A Matter Of Integrity, he uses examples of his own ministry to illustrate how he has become increasingly aware of the suffering of homosexual people within the church, but also puts it down to his growing understanding of the Christian Bible.
He writes: ''Rather than condemn and exclude, can we dare to create an environment for homosexual people where issues of self-esteem and wellbeing can be talked about; where the virtues of loyalty, respect, interdependence and faithfulness can be nurtured, and where exclusive and permanent same-sex relationships can be supported?''
And he questions why so many Christians are prepared to dismiss biblical suppression of women in leadership, or the scriptural endorsements of the slave trade as ''cultural'', but not of negative references to homosexuality.
He said: ''It is my duty to ensure that everyone - gay or straight - knows that I believe God is for them.
''If the church in this country wants to be at the forefront of delivering social provisions, we have a responsibility to ensure that everyone knows the services we provide are for them.
''However, this commitment to inclusion is not just necessary in order to play a role in today's society; it is, in my view, the most biblical way of mirroring the life of Jesus Christ.''
The support service he has established includes videos discussing the issues and case studies of people who have been affected by them.