Religious beliefs must not influence the curriculum, faith schools warned.
Faith schools must teach sex education in accordance with the national curriculum, even if that contradicts their own religious beliefs, says Ed Balls.
The Children, Schools and Families Secretary told MPs this week that it was important schools gave a consistent message to pupils in sex education classes.
At the launch of the 10-year Children's Plan, ministers criticised the quality of some sex education, calling it "pretty atrocious".
Mr Balls told the House of Commons children, schools and families committee that Catholic schools had to teach sex education in the same way as every other school.
"It's an area where it is important there is consistency and that all children in all schools are given the proper guidance and support," said Mr Balls.
His comments followed the publication of a controversial document by Patrick O'Donoghue, the Bishop of Lancaster, which urged Catholic schools in his diocese to take a harder religious line.
Bishop O'Donoghue told schools that they should not take a neutral approach to lessons about safe sex. He quoted a document that called it "an immoral policy based on the deluded theory that the condom can provide adequate protection against Aids". Schools should also ban fundraising for Red Nose Day and Amnesty International because they "advocate" abortion, the bishop told his flock.
His document, "Fit for Mission", has received Vatican backing.
In a shift away from the pro-faith school message under Tony Blair, the former prime minister, Mr Balls said it was not his policy to expand the number of religious schools.
"We are not leading a drive for more faith schools," he told the Commons committee.
Mr Balls insisted any expansion in the number of faith schools was a local decision.
Barry Sheerman, the Commons committee's chairman, said some local authorities were finding it difficult to deal with the independent direction of Catholic schools. He claimed some dioceses had decided not to participate in multi-faith academies.
Mr Balls responded: "If those messages are being sent - that individual schools should go it alone - that would certainly worry me."
Faith schools had an important part to play in contributing to community cohesion, the minister said. Last year he launched "Faith in the System", which paved the way for an expansion in the number of religious schools, including increasing the number of private Muslim schools joining the state sector.
Mr Sheerman told The TES that members of the Catholic Church espoused two very different views. Some would discuss sex issues from a neutral point of view, then put the Catholic position and leave it for pupils to decide. Others supported the stance of the Bishop of Lancaster.
"These are two very strong competing voices," he said. "There is little evidence that increasing faith school numbers is the right option. What is the justification when I hear experts say it is integration, not segregation, that we need?"
Mr Balls managed to raise a laugh from the committee by not knowing the colours of the rainbow. One member asked him why the cover of the Children's Plan booklet had only six colours.
Mr Balls apologised for the absence of pink before being told the missing colour was in fact indigo. "I was speaking of the song," Mr Balls explained, to much amusement.