A territory submission on the second draft of the coalition's religious discrimination bill - attributed to Andrew Barr - said it was unclear whether it would let health practitioners refuse people medical treatment on religious grounds.

"[The bill] may protect a general refusal to provide contraception or hormone treatment ... potentially permitting indirect discrimination against groups such as women and transgender persons," Mr Barr said in the submission.

"It is [also] unclear whether ... [it] would empower a health practitioner to object to providing treatment that uses, or relies on research that did use, certain animal by-products or stem cells."

The bill also left open the possibility that "religious bodies" - including hospitals, aged care, and accommodation facilities - could discriminate against prospective employees on religious grounds, Mr Barr said.

He said the bill could see large employers face barriers to intervening in employees' behaviour, as comments informed by religious beliefs would have to be dealt with outside of any existing code of conduct.

While workers' statements couldn't be warranted if they were malicious or potentially intimidating under the bill, it didn't go so far as to say any national, racial, or religious hatred was out of order, Mr Barr said.

"The ACT government is concerned [the bill] would limit the capacity of employers to maintain tolerance and diversity in Australian workplaces."

Territory legislation allows schools to discriminate against students on religious grounds at the time of admission, but the proposed bill left open the possibility for religious discrimination at any time, Mr Barr said.

It did not call for students to be discriminated against because of their gender or sexual orientation.

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Mr Barr said one clause in the bill sought to protect all religious "statements of belief" from any discrimination claim under Australian, state, or territory law - overriding the ACT's ability to evolve the law in response to the community's needs. The statements of belief had to be made "in good faith".

The government feared the clause - among others in the bill - prioritised religious freedom "to the detriment" of other human rights, Mr Barr said. It also would make it harder for employers to abide by their legal obligations and maintain "safe and harmonious" workplaces.

"Noting that statements of belief could be both written and oral, it is unclear how an employer would be able to separate out lawful statements of belief from unlawful discriminatory conduct," Mr Barr said.

The second draft of the religious discrimination bill was released on December 10, 2019, after 11 changes were made to the first draft. Labor was not consulted about the second exposure draft.