Children aged 13 who consult a doctor for advice about contraception, abortion or sexually transmitted diseases are entitled to be treated without the knowledge of their parents, the General Medical Council (GMC) will say today.

In its first guidance on the treatment of children up to the age of 18, the GMC says children of 12 or under are presumed in law not to be capable of giving consent and doctors should normally disclose details of any sexual activity involving them to a third party.

But where a child is over 13, and efforts to persuade them to tell their parents fail, advice or treatment should be offered in confidence, unless there are reasons to believe the sexual relationship is "abusive or seriously harmful".

Rosalind Ranson, who chaired the committee that produced the guideline, said: "Doctors should always act in the best interest of the child but sometimes there is a conflict between their duty of confidentiality and their duty of disclosure in the public interest or to protect the child."

But Michaela Aston, spokeswoman for the anti-abortion charity Life, described the new guidelines as "outrageous". "No doctor knows a child like its parents do," she said.

Research carried out by Brook, the young people's sexual advice service, found confidentiality fears deter a quarter of sexually active under-16s from seeking medical advice.