The Liberal Democrat did vote in favour of the government bill, which was passed this week and will allow trans and gender diverse Victorians to choose the sex on their birth certificates.

But before that moment, he tried to introduce a completely different idea.

Mr Quilty said birth certificates should not have a sex listed at all, unless it was specifically requested.

"Unfortunately government is not indifferent towards our sex. The government cares about your genitals, and it should not," he said.

"We can decide for ourselves whether we think someone is a man or a woman.

"We do not need the government's help in figuring it out, and it is OK if we do not all agree.

"I believe that what your gender is and what is inside your underwear is none of the government's business."

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The amendment was not supported in the upper house by either the government or opposition.

Labor MP Jaala Pulford said removing sex descriptors from birth certificates would cause problems at times such as reporting to the Australian Bureau of Statistics.

"Such a wide-ranging set of consequences would need to be properly considered, investigated and consulted on with the community, and we are certainly not in a position to support that at this stage," she said.

The change to birth certificate legislation passed with support from North East MPs Tim Quilty and Jaclyn Symes, but Tania Maxwell from Derryn Hinch's Justice Party voted against the change.

Mr Quilty was critical of the government for how it has handled the controversial debate.

"Instead of addressing concerns and bringing the community with them, they wave their arms around and cry 'bigot' at those who do not share their views," he said.

"This is not the green left university club where people can just be dismissed because you do not like what they have to say."