The Scottish Human Rights Commission has told the Government its draft guidance on sex education does not properly recognise that, when a parent is against the teaching of such material, the child's right to effective education is "paramount".
Its memo came after a Scottish Government-commissoned survey found secondary school children had a "worrying" attitude towards sex, with more than one-quarter not understanding that "no means no".
The study of more than 1000 pupils found nearly 20% did not know using condoms could help to prevent sexually transmitted infections.
The commission said the European Convention on Human Rights, which came into force in 1953, states the parental right to ensure education according to religious and philosophical convictions is subsidiary to the child's right to education.
It said: "The commission is unconvinced that the approach in the draft guidance to encourage schools to provide comprehensive RSHP (Relationships, Sexual Health and Parenthood) education is sufficient to fulfil the duty of the state to realise the right of every child to such education."
The European Convention on Human Rights states no-one shall be denied the right to education and includes a duty on a State to respect the right of parents to ensure education according to "religious and philosophical convictions".
However, the European Court of Human Rights has held that, where the beliefs of the parents conflict with the child's right to an effective education, the child's right will prevail.
The United Nations Convention on the Rights of the Child, which has been legally binding on the UK since 1991, upholds the right to health education. The UN Committee on the Rights of the Child has said children and young people have the right to effective sexual and reproductive health education in a manner appropriate to their age and stage of development.
However, evidence presented to a Scottish Parliament health and sport committee inquiry into teenage pregnancy has called relationship and sex education patchy, inconsistent and mixed.
NHS Health Scotland was "particularly critical", arguing there was no requirement to deliver more than the "bare minimum", while the Scottish Sexual Health Lead Clinicians Group said there was "no monitoring and accountability, nor sanctions in place for non-compliant schools, and schools are free to determine content".
The Scottish Human Rights Commission added: "The guidance should ensure appropriate emphasis to the best interests of the child as a primary consideration, the evolving capacities of the child and the child's right to participate in decisions with their views given due weight.
"Where a real or perceived conflict between the rights of the child and the rights of parents in this area arises, it is these general principles of the UNCRC (that) should provide the guiding framework for decisions.
"It is the child's right to effective education that is paramount."
A Scottish Government spokesman said: "The Scottish Government is revising the guidance on relationships, parenthood and sexual health education.
"We invited comments on the draft guidance and will consider all responses. Through Curriculum for Excellence we are able to ensure pupils have an understanding of a variety of beliefs and opinions and use this to encourage confident, capable young people who can form healthy, respectful relationships with others."