Dr McGirr moved an amendment and said it would be "highly problematic" if health practitioners faced new requirements to participate in treatments they disagreed with under a bill to decriminalise abortions in NSW.

"Under the bill as it stands, if a medical practitioner has a conscientious objection to either termination in general, or termination under certain circumstances after a particular gestational age or a gender selection unrelated to medical reasons, they are duty bound to refer the patient," he said.

Dr McGirr said the Medical Board of Australia's code of practice already instructed doctors that their personal or religious objections should not impede their patients getting access to legal procedures.

"Termination is not the only procedure to which a medical practitioner may have a conscientious objection where the procedure is legal and even normalised in some jurisdictions," he said.

"Would it be reasonable to have these requirements for other procedures, for example ... male circumcision?"

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Dr McGirr said practitioners should still "facilitate access to a second opinion".

In response, Health Minister Brad Hazzard said "everyone was entitled to their religious views" but "doctors have an obligation for their patients getting referred".

Earlier in the day, Dr McGirr voted against the entire bill on its second reading, but it still passed with a 23-seat majority and debate moved on to the 19 proposed amendments.

At the time of publication, a final vote was predicted to occur late on Thursday night.