Supporters claim the academies, the first of their kind in the UK, would meet parental demand for faith-based education while promoting greater understanding between religions.
But secular organisations described the plans as impractical. Two years ago proposals for a multi-faith secondary in central London collapsed over the practical difficulties of providing schooling on one site for different religions.
The proposed school would have educated 1,000 pupils in Westminster. Boys and girls would have been taught separately but mixed in the playground - something Hindu, Christian and Jewish backers were happy with, but Muslim supporters were not.
However, the Multi-Faith Secondary School Trust charity, which was behind the Westminster project, and is supported by the country's main religious organisations, has now won support from the Department for Education and Skills to sponsor a similar school elsewhere.
Jacqui Smith, schools minister, said in a speech to a Church of England conference last monath that there was "exciting potential for multi-faith academies".
She said civil servants were in talks with the trust, which lists Richard Harries, the Anglican bishop of Oxford, and Rabbi Jonathan Wittenberg, from the New North London Synagogue, among its backers.
Richard Gold, education lawyer and trust secretary, said London, Birmingham and Manchester had been identified as possible sites. The academies would be for boys and girls of two or three faiths, depending on location. The trust, which would sponsor and support the schools, says it would be impractical to cater for more than three religions.