A report on citizenship education, published yesterday by the Commons education select committee, said there was "little concrete evidence" that provocative topics were being tackled responsibly by faith schools.
Gordon Marsden, a committee member and Labour MP for Blackpool south, said schools had a duty to present a broad spectrum of views.
"Faith schools have a responsibility to make it clear that, in 21st-century Britain, there are differing views," he said.
"Their attitude is 'trust us to do it'. But we need verification."
Andrew Copson, education officer at the British Humanist Association, said there was concern that citizenship-related topics were being taught in religious education, so that faith schools could impose their views.
But Dr Mohamed Mukadam, chair of the Association of Muslim Schools, defended faith schools in his evidence to the committee. He said that, although the Koran classified homosexuality as sinful, "it would be wrong to translate that as homophobic. I do not think the Koran teaches that people should go around beating up homosexuals," he said.
Vincent Nichols, Archbishop of Birmingham, told MPs that Catholic schools taught the subject in a "mature and proper fashion", adding that there was a clear distinction between having a moral objection to homosexuality and attacking gay men and women.
The committee said that citizenship education was "patchy at best", with only a quarter of schools providing the subject at the highest standard and a quarter delivering below-par lessons.
Professor Sir Bernard Crick, who led the introduction of citizenship, said it was "too early to judge" its success.
The committee's report also recommended making school councils mandatory in England, as they are in Wales. Around 94 per cent of heads in England said they had school councils, although only half of pupils recalled electing them.