Premier Daniel Andrews' department quietly ordered an investigation into the office of FOI commissioner Lynne Bertolini in April, after a complaint was raised regarding internal matters that the government is refusing to disclose.

Department boss Chris Eccles recently told a parliamentary committee that the allegations were "sufficiently serious" enough to initiate a review by former public sector standards commissioner Peter Allen – the same senior bureaucrat who has since been called in to help investigate embattled minister Adem Somyurek amid claims of bullying and harassment.

But while mystery surrounds the details of the inquiry, the government has not ruled out removing Ms Bertolini as part of a broader shake-up of her office.

Such a move would make the inaugural FOI commissioner the latest in a growing line of senior public servants or board officials who have either resigned or been sacked since the Andrews government won the state election in November.

Ms Bertolini was appointed under the Baillieu government three years ago, in a move the Coalition promised would "end the culture of secrecy" within state departments and give the public more access to information about the government.

But the office was branded a toothless tiger because it did not have the ability to review decisions by ministerial offices or department heads, and at one point, was unable to meet its own review deadlines because of the volume of requests and a general lack of staff.

Labor went to the election promising to revamp the agency by replacing it with a new organisation – the office of the public access counsellor – which will subsume the functions of the FOI commissioner, but also have the power to review ministerial and departmental decisions to not release documents under the often used "cabinet-in-confidence" exemption.

However, when asked if Ms Bertolini would be reappointed as the public access counsellor, a spokeswoman for Special Minister of State Gavin Jennings replied: "The appointment of the public access counsellor will be a matter for consideration once the necessary enabling legislation has been passed by the parliament."

The lack of transparency surrounding the review into the FOI commissioner's office has left the government exposed to claims it is paving the way for yet another senior departure.

In the past six months, a number of high-profile departures have occurred, including the sacking of Worksafe's chief executive Denise Cosgrove and chairman David Krasnostein over the Fiskville CFA centre; the resignation of Peter MacCallum Cancer Centre chair Wendy Harris after a stoush over private beds at the hospital; and the spilling every water board position in the state, amid governments concerns that members were not doing enough to tackle climate change.

"Labor must explain why it is having a secret inquiry into the independent FOI commissioner. This risks being just another witch-hunt to force out an independent officer," said opposition spokesman Gordon Rich-Phillips.

Details of the review into the office of the FOI commissioner first emerged during a parliamentary budget hearing last month, when Mr Jennings was asked about the matter by Liberal MP Tim Smith.

The minister deferred to department secretary Mr Eccles, who told the committee: "There were certain matters that were brought to my attention, and it is not appropriate to disclose the detail, which I considered to be sufficiently serious to call upon the public service commission to initiate an inquiry. That inquiry is on foot, and the matter is before government. I have probably nothing more that I can usefully add."

Despite promising to be more open and accountable than its predecessors, the government has continuously refused to discuss details about the inquiry, including whether the complaint was specifically against Ms Bertolini, or a member of her staff.

Ms Bertolini declined to comment, but it is understood she co-operated with the inquiry, which focused on the internal administration of her office.