Free schools could prove to be "risky and divisive," the association representing the majority of primary heads has warned for the first time.
The NAHT has claimed that the new wave of state-funded independent schools risk increasing segregation by "hiving off" pupils with different religions from comprehensives. It is also concerned that free school projects will be dominated by middle-class parents, reducing the social mix of other state schools.
The association's position on free schools comes after it accepted the Government's policy on academies, as so many of its members were becoming involved with them.
NAHT president Mike Welsh was one of the first heads to turn his Swindon primary into an academy earlier this term.
Russell Hobby, general secretary of the association, said: "We have been moderate on academies, but that doesn't mean we extend it to the whole of the Government's agenda on structural change.
"You are setting up schools based around a particular view of the world, which could possibly be faith-based. You also have schools that hive themselves off.
"Every school should respond to what the parents in the community want, but education is not a customer service-type environment. The comprehensive ideals about learning alongside each other are important."
Mr Hobby said the dominance of middle-class parents behind many of the free school projects was "as much of an issue" as faith-based segregation of pupils.