In August the Supreme Court ruled that Ombudsman Deborah Glass had jurisdiction to investigate the alleged rorting use of taxpayer funded electoral staff to work on Labor's election campaign in 2014.

The state government has already spent tens of thousands of dollars on Supreme Court fees this term.

But on Thursday afternoon the Andrews government said it would appeal the court's decision to "protect the architecture of Victoria's integrity regime".

The legal action has fuelled speculation that Labor is trying to delay any investigation until after the next election.

Acting Attorney-General Steve Herbert said in a statement that the government was concerned the court's decision had significant resource implications for the Ombudsman and would impact her ability to conduct investigations into other matters.

Mr Herbert said if the decision went unchallenged there would be no impediment to one house of Parliament referring members of the other house to the Ombudsman for any matter.

Shadow Attorney-General John Pesutto said the latest action showed Labor knew it had rorted entitlements and called on the ALP to foot the growing legal bill, not taxpayers.

"Daniel Andrews shouldn't have anything to fear if there is nothing to hide," Mr Pesutto said.

"It's hard to know what's worse, the Andrews Labor government arrogantly refusing to accept the court's decision that an independent investigation proceed, or the fact that the government will waste hundreds of thousands of taxpayer dollars doing it."

Victorian Greens leader Greg Barber said he believed the government was trying to delay the investigation until after the next state election.

"If I was in their position I'd want an investigation to clear the air," he said.