In a speech to the NASUWT teachers' union, Mr Hunt said schools should not have "gender-based segregation" and that teachers must not be "undermined".
Mr Hunt welcomed Birmingham council's investigation into the "so-called Trojan Horse conspiracy".
The Department for Education is also examining claims of schools being "taken over" by Muslim hardliners.
The inquiries follow an anonymous letter alleging that factions within the Muslim community were seeking to gain influence over schools in Birmingham.
[A COMMENT] There should be no place for religion in schools. It is indoctrination of children. France have got this right.
[ANOTHER] Welcome to the reality of out-of-control immigration in Britain. You are reaping what you sowed. [BBC] Read more
