The Council of Europe reported that children born with characteristics of both sexes must not be subjected to "normalization" surgery without their consent.
The human rights organization also urged states to stop classifying people under the male-female binary.
"Intersex children are (too often) subjected to unnecessary surgical interventions and medical treatments without their consent," said Council of Europe Commissioner for Human Rights, Nils Muiznieks. As a result of surgeries or other sex-altering medical interventions, intersex people are denied their right to physical integrity as well as their ability to develop their own gender identity, as an a priori choice is made for them," he said, urging an end to what he branded an "unacceptable situation".
According to US researcher Anne Fausto-Sterling, some 1.7% of children are born with intersex characteristics. They may be born with both ovaries and testes, or they may have hormonal balances that do not allow for an obvious sex classification.
Parents are often ill-informed by medical specialists, and put under pressure by state institutions to choose a gender for their newborns, Muiznieks said, adding that they then subject them to irreversible surgery.
Noting a high suicide rate among people who had been subjected to gender-attribution surgery, the paper "calls on member states to end medically unnecessary 'normalizing' treatment of intersex persons when it is enforced or administered without the free and fully informed consent of the person concerned".
European states must also "facilitate the recognition of intersex individuals before the law... while respecting intersex persons' right to self-determination", it said.
"National and international medical classifications which pathologize variations in sex characteristics should be reviewed with a view to eliminating obstacles to the effective enjoyment, by intersex persons, of human rights," it added.
Finland and Portugal are currently the only countries in Europe that do not impose a time limit for registering the sex of a child if it cannot be determined at birth. In France, parents have up to three years to register the child's sex in exceptional cases. In Belgium, the sex of a child is usually registered within a week, and within three months at most in intersex births.
Germany allows parents to leave the sex classification of a newborn open until it is resolved, however a birth certificate is not issued in the meantime, leading to problems with parental benefits, insurance and other issues.
In his recommendations, the commissioner said "sex assignment treatment should be available to intersex individuals at an age when they can express their free and fully informed consent. Intersex persons' right not to undergo sex assignment treatment must be respected," Muiznieks added.
The Council of Europe is a human rights organization that includes 47 member states, 28 of which are EU members.