The proposals are part of the plans – also backed by Plaid Cymru – to reform the Senedd with more politicians.
Separate planned legislation will expand the size of the Senedd from 60 to 96 politicians.
There are already concerns, held by Welsh Parliament Presiding Officer Elin Jones, that the gender equality proposals are not in the powers of the Senedd.
That would not stop the bill being passed, but it raises the prospect of the legislation being argued over in the courts.
Parties will need to draw up lists of candidate for election, listed in order of who will be elected first.
The EHRC’s concerns were raised in a letter to the Welsh Parliament committee looking at the reform plans, saying the bill “may lead to the inclusion of quotas based on a person’s self-identified gender as opposed to their legal sex”.
Interim chief executive John Kirkpatrick said this might be inconsistent with the Equality Act 2010.
He told the Senedd reform committee the anti-discrimination law sex was a person’s legal sex, as stated on their birth certificate or acquired through a gender recognition certificate.
Candidates would need to declare their gender in a statement. Mr Kirkpatrick said it was unclear how that would work in practice.
He said if this means self-identified gender, “this is unlikely to be lawful as not all those who self-identify as women will be considered to be legally be so under the [Equality] Act.”
“If ‘gender statements’ refer to a statement of one’s legal sex this should be made clear.”