The Government said parents could delete parts of the agreement they disagreed with - a significant ruling as all schools now have to have these documents specifying their aims and values, expectations and responsibilities.
Hathern primary in Loughborough included the promotion of Christian values as an aim. Parent Eric Goodyer objected because the chool was the only one available.
"Many schools will have pupils of different faiths and will want to give sensitive consideration to discussions arising from issues that relate to this," said a Government official.
Mr Goodyer said: "I find it astonishing that a publicly-funded body could have issued such a document. You cannot ask parents who are not Christian to sign a document that requires them to affirm their support for a religious ethos that is not their own."