A new regime for conscientious objection will allow doctors to refuse treatments, such as prescription of hormone-replacement therapies to transgender patients, on religious grounds, provided they refuse to provide the treatments to all their patients.

The first draft of the Religious Discrimination Bill being pushed by the Federal Government has undergone a major rewrite, amid concerns it allowed health professionals to discriminate against patients based on their race, sexuality, gender or disability.

On Tuesday, Attorney-General Christian Porter revealed a new version that he said made it “absolutely clear that the conscientious objection of a medical professional has to be to a procedure, not to an individual person”.

Mr Porter told reporters in Sydney that under the Bill, it would be acceptable for a GP to refuse to “engage in hormone therapies” for a transgender patient, or for a pharmacist not to dispense contraception, but that the decision could not be based on the provision of a service to a particular individual patient.