The London authority where the school would have been built is instead to opt for a non-religious city academy, dashing the hopes of those who believed the secondary could become a flagship of inclusive, faith-based education.
The proposed school, backed by leading names from the Muslim, Jewish, Christian and Hindu communities, would have educated 1,000 pupils in Westminster.
High-profile supporters include Richard Harries, the Bishop of Oxford, and Rabbi Julia Neuberger, chief executive of Kings Fund.
Westminster council is set to reject the scheme at a meeting later this month. Tim Joiner, cabinet member for education, criticised the multi-faith-school proposals as insufficiently thought-through.
The council claims their were disagreements over how pupils of different religions and sexes were to be educated. Boys and girls would have been educated in separate lessons. Although the school's Hindu, Christian and Jewish backers were happy to have both sexes mixing in the playground, its Muslim supporters were not.
The multi-faith scheme also proved marginally less popular than a city academy among residents who responded to a council survey.
Mr Joiner said: "I am sure this will be disappointing for the many people who would have loved to have seen a multi-faith school in Westminster. The idea is a good one and I am sure it will happen somewhere in this country."
Stephen Barlow, of the National Union of Teachers' Westminster branch, said it would have been impossible to have offered separate classes for boys and girls of each religion.
Rabbi Jonathan Wittenberg, from the New North London Synagogue, who drew up the plans, denied there had been disagreement between the religious groups.
He said that heads had resisted the plans. "We have been struck by this assumption that the community comprehensive provides everything for everyone. There was an unwillingness to see that perhaps it doesn't."