Medical leaders clashed yesterday over a plan to extend the right of doctors to refuse treatment to patients where they have a conscientious objection.

The British Medical Association accused the General Medical Council, the doctors' disciplinary body, of undermining fundamental ethical principles in proposals that could give doctors a licence to discriminate against certain groups of patients, including same sex couples, Jehovah's Witnesses and alcoholics.

The only legal right is for doctors who do not wish to participate in abortions, enshrined in the Abortion Act.

It is also widely accepted that some doctors are not to be involved in prescribing contraceptives such as the IUD and the morning-after pill and in withdrawing life-prolonging treatment. The GMC has been under pressure to revise its guidance on conscientious objection to accommodate doctors with other personal beliefs.

The draft guidance says doctors must not discriminate against patients because of their sexual orientation, gender or race. But it adds "unnecessary restrictions" should not be imposed on doctors because of their "cultural preferences or religious or other convictions".

The BMA said that was ambiguous and could confuse patients. Same-sex couples might be refused IVF treatment or a Jehovah's Witness could be refused treatment by a doctor who did not agree with their belief, the association said. It added it had anecdotal evidence of medical students claiming conscientious objection to learning about the clinical impact of alcohol.

Tony Calland, chairman of the BMA's medical ethics committee, said: "Doctors are not there to judge patients but to treat them."