Victoria’s emergency commissioner has quit amid workplace bullying allegations, with the government saying his behaviour falls “well short of expectations”.

Emergency Management Commissioner Craig Lapsley resigned effective immediately on Tuesday after spending weeks on leave.

“It is on the public record that there had been a WorkSafe investigation into workplace issues within Emergency Management Victoria,” Deputy Premier James Merlino told reporters.

“Mr Lapsley himself has acknowledged that his behaviour has fallen well short of expectations,” Mr Merlino told reporters.

“From a personal point of view as minister for emergency services, I am disappointed. This is an outcome that no one wanted, but this is the appropriate course of action.”

Appointed in 2014, Mr Lapsley late last year apologised for bullying claims levelled against senior staff in the organisation.

Mr Merlino said there had been issues for “a little while” and the matter came to a head as Mr Lapsley took leave amid a WorkSafe investigation.

“I had a direct discussion with Mr Lapsley that I as (emergency services) minister would not tolerate bullying behaviour in the workplace,” Mr Merlino said.

WorkSafe could not comment except to say it was continuing to look at allegations of bullying within EMV.

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

-AAP