The move came after Deputy Opposition Leader Rob Hulls accused the government of having a dinosaur-like attitude on the issue.
His electorate officer, Jaclyn Symes, who is due to give birth next month, was refused 14-weeks paid maternity leave by Liberal speaker Ken Smith.
She worked as an adviser to Mr Hulls while he was deputy premier, and transferred to a position in his electorate office after Labor lost the November election.
Her annual and sick leave transferred over, but her maternity leave is at Mr Smith’s discretion.
Mr Smith wrote to Ms Symes saying she had not completed 12 months’ continuous service with the parliament and was therefore ineligible for paid maternity leave.
The premier on Thursday ordered Public Sector Standards Commissioner Peter Allen examine the employment policies to resolve any inconsistencies.
Mr Baillieu said Labor introduced the maternity leave policy in 2002.
“I believe that policy is unreasonable,” he told parliament.
“I believe that there should be recognition of prior service for the purpose of paid maternity leave between the public and parliamentary services.”
Mr Baillieu said he believed the anomaly will be fixed and Ms Symes would be paid maternity leave.
Ms Symes said she was surprised by Mr Smith’s decision.
“I just thought he would do the right thing,” she told reporters.
“His decision is unfair.”
Mr Hulls demanded Mr Smith reconsider his decision, given Ms Symes has worked in his office for more than five years.
“The speaker and in fact the coalition might have Jurassic Park views about maternity leave, but for goodness sake, it is 2011, and women are entitled to maternity leave,” he said.
“This is just an outrage, it’s clearly discriminatory, and one wonders whether the speaker isn’t purely playing politics with this young woman’s pregnancy.”
Mr Hulls said Mr Smith should not let his ill feelings about him influence his behaviour towards others.
The Community and Public Sector Union is taking action on Ms Symes’ behalf in Fair Work Australia, the national workplace relations tribunal.
The issue sparked heated exchanges in parliament, with the opposition demanding Mr Smith vacate the Speaker’s chair during debate on the matter because he had an inherent interest.
But Mr Smith refused to vacate the chair saying he had no interest in the matter.
Mr Allen said he expected to provide his report within a fortnight.
Comment was being sought from Mr Smith.