The South Australian Opposition has accused Labor's right faction of deliberately scuttling the Premier Jay Weatherill's attempt to pass gender identity laws.

The bill would have made it easier for people to change the gender on their birth certificates, but it was defeated last night in a conscience vote.

The vote was taken while Mr Weatherill was travelling home from a trip to Finland, and Opposition Leader Steven Marshall said Labor's right jumped on the opportunity.

"This is something that's obviously very important to the Premier and for his own party to essentially bring on the vote well before it was required and then vote it down," Mr Marshall said.

"The right faction of the Labor party were seriously against the Premier on this bill and they used every opportunity to make sure it was defeated."

Labor MPs missed vote

Several members who would have supported the bill were absent from the chamber when the vote was taken.

That included Liberal MP David Pisoni, after Speaker and senior right faction member Michael Atkinson banned him from Parliament over his interjections during question time.

But Mr Weatherill denied there was a deliberate move from within his party to defeat the bill.

"If those MPs chose to vote against it, it's a matter for them. I don't reflect on them and I don't think it reflects on me," Mr Weatherill said.

The Premier admitted he had not expected the bill to be dealt with so soon.

"It was a surprise to me to see it presented at a time when there wasn't support for the legislation," he said.

"There is a majority of people that support it but for circumstances some of the people weren't in the chamber. I understand the vote was advanced on the basis it was expected to pass."

Mr Weatherill said Parliament had the numbers to pass the bill, and it would be reintroduced later in the year.