Pupils will learn about all types of relationships
Children's Secretary Ed Balls has denied plans for compulsory sex education in England's schools have been watered down.
But an amendment to a government bill gives faith schools more freedom to tailor teaching to their own beliefs.
Pressure groups claim this amendment would allow faith schools to ignore requirements in the bill to teach it in a balanced way, respecting diversity.
The government has denied it could result in a rise in homophobia.
If a school doesn't approve of contraception or abortion or homosexuality, then it can give that message
Rabbi Dr Jonathan Romain Accord coalition
Mr Balls dismissed suggestions the amendment to the Children, Schools and Families Bill, which was first revealed by the BBC News Website, represented an "opt out" for faith schools.
He told the Today programme: "A Catholic faith school can say to their pupils we believe as a religion contraception is wrong but what they can't do is therefore say that they are not going to teach them about contraception to children and how to access contraception.
"What this changes is that for the first time these schools cannot just ignore these issues or teach only one side of the argument.
"They also have to teach that there are different views on homosexuality. They cannot teach homophobia. They must explain civil partnership."
But opponents say this requirement was already in the Children, Schools and Families Bill.
Rabbi Dr Jonathan Romain, of the Accord Coalition which calls for an end to what it sees as religious discrimination in school staffing and admissions, told Today he was "astonished and saddened" that Mr Balls had chosen to effectively give faith schools an opt-out.
The case for and against
"If a school doesn't approve of contraception or abortion or homosexuality, then it can give that message or it can omit certain facts.
"We know there are some faith schools which take a very negative view."
Under the plans, all schools are to be required to teach children aged seven to 11 about relationships including marriage, same sex and civil partnerships, divorce and separation under Personal, Social, Health and Economic Education.
Secondary school pupils are to learn about sexual activity, reproduction, contraception as well as same sex relationships.
Sex and relationship education - who does what?
Age 5-7 - puberty, relationships and how to keep safe
Age 7 - 11 - puberty, relationships including marriage, divorce, separation, same sex and civil partnerships and managing emotions and dealing with negative pressures
Age 11 - 14 - Sexual activity, human reproduction, contraception, pregnancy, STDs including HIV/Aids and high risk behaviours, relationships, including those between old, young, girls, boys and same sex
Age 14 - 16 - Body image and health, choices relating to sexual activity and substance misuse, and the emotional well-being, reducing risk and minimising harm, parenting skills and family life, separation, divorce and bereavements, prejudice and bullying
The bill states the subject is to be taught in a way that promotes equality, accepts diversity and emphasises both rights and responsibilities.
This requirement could have been problematic for schools governed by religions that are specifically opposed to homosexuality and contraception. About a third of schools in England are faith schools.
In a statement on its website, the Catholic Education Service says the amendment, which was tabled by Children's Secretary Ed Balls, was secured after a period of "extensive lobbying".
But it refused to comment on the issue.
Liberal Democrat Children's spokesman David Laws said the amendment was "a serious and undesirable U-turn".
He told Today: "This government hasn't had a bad record over the years in trying to challenge things like homophobia.
"Now, with this amendment it's undermined a lot potentially, that it's been achieving. I think it will upset many people who believe that in today's Britain we should have a society where the taxpayer should not be subsidising prejudice."
The British Humanist Association is also among those who have criticised the amendment.
Its chief executive Andrew Copson said the amendment effectively gave a licence to faith schools to teach sex and relationships educations in ways that were homophobic, gender discriminatory and violated principles of human rights.
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