The head of Victoria's emergency services has resigned, admitting his workplace behaviour was "abrasive and confronting".

Emergency Management Commissioner Craig Lapsley offered his resignation to Deputy Premier and Emergency Services Minister James Merlino.

In a statement, Mr Merlino said it had recently become apparent that Mr Lapsley had "not always conducted himself in accordance with the very high standards expected of him".

"As a result, the EMV [Emergency Management Victoria] workplace has been very difficult and challenging for a number of his staff," Mr Merlino said.

"I have previously made it clear to Mr Lapsley that bullying and inappropriate workplace behaviour will not be tolerated and that remains very firmly the case."

In a statement, Mr Lapsley said he was aware of the criticism of his conduct.

"I recognise and acknowledge that on occasion I engaged in inappropriate workplace behaviour that was abrasive and confronting and that I did not treat people with the great respect they deserved,'' Mr Lapsley said.

"Upon reflection I believe I could have done much more to show and communicate my unquestioned admiration of, and support for the people who are at the heart of the State's emergency response system.

"I deeply regret the instances where my conduct fell short of the very high standards expected of me, and I apologise sincerely to those people affected."

WorkSafe Victoria has received complaints about senior management at EMV.

"WorkSafe is continuing to make inquiries into complaints of bullying behaviours at EMV," a spokesman said.

"It would be inappropriate to comment further at this stage."

Mr Lapsley had been commissioner for four years, and the Government thanked him for his contribution in "a critical and challenging role", through which he helped improve Victoria's emergency preparedness, response and recovery capability.

"Through EMV's efforts, Victoria is undoubtedly much better prepared for the emergencies it will inevitably, albeit unfortunately, face in the future," Mr Merlino said.

"It is my very strong view that all government employees, including those at EMV, should be able to work in safe and supportive workplaces."

Lapsley 'admitted behaviour was not up to standard'

Speaking at a later press conference, Mr Merlino said the resignation was effective immediately.

He said he would make an announcement about Mr Lapsley's replacement in the coming days.

The Deputy Premier was tight-lipped about the exact nature of the bullying investigation, saying only that they were serious matters and that Mr Lapsley himself had admitted his behaviour was not up to standard.

Mr Merlino said he became aware of the issues last year, but the WorkSafe investigation had taken place over the past few weeks and was about to conclude.

Mr Lapsley has been on leave throughout that period.

He had been at the helm of EMV during the long-running and bitter pay dispute at the Metropolitan Fire Brigade, and the fight over a proposed restructure of the Country Fire Authority.

Mr Merlino rejected any suggestion that politics had led to his resignation.

"These were serious issues, they warranted an investigation by WorkSafe. This is solely about workplace behaviour," he said.