The selection contravenes a fundamental principle of the NHS, it was claimed.
Staff working for the provider are required to sign up to its values and vision.
Manchester GP Dr Mohammed Jiva told the conference that Hope Citadel Healthcare, a social enterprise company, one of whose partners is the Salvation Army, has procured two GP-led clinics in Oldham and one GP-led health centre in Middleton, Manchester across two PCTs.
Hope Citadel's website makes it plain that the organisation is a specifically Christian organisation, Dr Jiva said.
Hope Citadel aims to provide spiritual care and health care ‘alongside and in conjunction with clinical care', to take into account ‘spiritual aspects' of wellbeing and to take ‘every opportunity' for spiritual development, he added.
Its vision involves ‘working with local churches and other Christian organisations, and developing ways of linking personal and community and spiritual activity with primary care services in order to offer whole-person healthcare,' he said.
The person specification for applicants for GP and practice manager vacancies stipulates as an essential criterion support for the vision and values of the organisation.
‘The NHS recognises all faiths and beliefs. Yet two PCTs have identified a preferred provider that recognises one belief over all others. This goes against the core principle on which the NHS was founded,' Dr Jiva said.
A spokesperson for NHS Heywood, Middleton and Rochdale said: 'Hope Citadel is a GP-led consortium which was awarded the Health Centre contract at Middleton following a rigorous procurement exercise that was delivered under a national process. The GPs who lead the consortium have provided services in the Middleton area for many years and their bid specifically addressed the varied health issues in that area.'
'The services it will provide will be accessible to all and absolutely not based on faith. Any suggestion that this is the case is inflammatory and without grounds".
In a statement emailed to Healthcare Republic, Hope Citadel said: 'Hope Citadel, a not-for-profit community interest company, is not a discriminatory organisation. We are committed to the vision and values of the NHS and will work with all sections of the community to provide the best whole person care for our patients.
'We currently have a number of community partners who have a christian faith base however, all of these organisations work with and help people of all backgrounds and beliefs. We have been open and transparent in our tender model which included the submission of our own vision and values as part of the assessment.'
Colin Scales, director of commissioning at NHS Oldham, said: 'We were very surprised to hear about these comments as they are completely unfounded.
'Over many years we have supported the continual development of primary care, working closely with local communities, GPs and their staff.
'We have always ensured that any services are accessible to all members of our different communities, alongside an assessment of any provider's abilities to deliver high quality clinical care.'
- Should PCTs select single-faith providers to run GP-led health centres?
Click here for our live blog from the LMCs Conference 2009