Mr Andrews office has been accused of directing upper house MPs to pool electorate officer entitlements in the lead-up to 2014's state election.

The staff are alleged to have campaigned at the election – instead of working to support MPs in their parliamentary and electorate duties, as they are meant to.

The Court of Appeal last month ruled Ombudsman Deborah Glass was free to probe the allegations against Labor.

The ruling came after the government attempted for a second time to use the courts to block Ms Glass from investigating the so-called "rorts-for-votes" scandal.

On Thursday afternoon, Attorney-General Martin Pakula said he would go to the High Court to challenge last month's decision.

Doing so, he said, would "protect the architecture of Victoria's integrity regime, particularly regarding the relationship between the Ombudsman and the Victorian Parliament".

The Court of Appeal's decision, a statement from Mr Pakula said, could see "a simple majority" of either house of the Victorian parliament "require the Ombudsman to conduct an investigation into any matter".

The opposition's shadow Attorney-General, John Pesutto, said the Victorian Parliament had made a perfectly valid referral under the Ombudsman Act.

Labor, he said, was now doing everything it could to stop this independent investigation, "to protect the Labor Party and those who orchestrated the … systematic rorting of parliamentary entitlements".

"The legal costs of Daniel Andrews' attempts to cover-up allegations of serious wrongdoing will now involve many millions of taxpayer dollars," Mr Pesutto said.

Greens leader Greg Barber said the High Court bid showed Labor would do anything to avoid a legitimate investigation.

"This is the third court action they've launched to try to block the Ombudsman. Instead of fighting it, they should be welcoming the investigation, as a way to clear the air," Mr Barber said.

"A lot of taxpayers money is being used up on these legal challenges – which is kind of ironic, given the original allegation was about misuse of public funds," he said.