A deal has finally been struck between Melbourne's fire brigade and the firefighters' union, with MFB president Andi Diamond quitting her post immediately following the agreement.

There has been a protracted, bitter and political battle over a workplace agreement for Melbourne's paid firefighters, which expired in 2013 and Thursday's deal is likely to reignite political tension.

For years MFB management had been resisting the union's position, including trying to water down the previous workplace deal.

The MFB had been steadfast in resisting the union deal over concerns that the UFU wielded too much power and the EBA entrenched a lack of diversity.

Former minister Jane Garrett backed the management in its resistance to some provisions in the agreement — she resigned in 2016 over a similar impasse with the CFA after Premier Daniel Andrews supported the UFU-backed agreement.

The MFB board agreed to the new workplace agreement on Thursday night as the state sweltered.

In a short statement, Dr Diamond confirmed she had tendered her resignation to Emergency Minister James Merlino.

"I respect and accept the MFB's decision to agree to the in-principle signing of the Enterprise Agreement but as a result do not feel it appropriate for me to continue as president," she said

"I sincerely hope this is the beginning of rebuilding the organisation. I thank Minister Merlino for the opportunity to serve as president and I wish he, the board and staff well."

The standoff between the MFB management, and previously the CFA management and the union, has been a thorn in the Andrews Government and has left the Premier open to attacks that he is doing cosy deals with a union.

Firefighters have maintained throughout that their workplace deal is designed to protect firefighter and community safety.

The protracted dispute and the nature of some of the political attacks, including on the union, has sent morale among firefighters plummeting.

The Labor Government acknowledged for some time that there have been cultural issues in the state's fire services, it also proposed a bold overhaul of fire boundaries last year but does not have the numbers in Parliament to pass the reforms.

On Thursday night Mr Merlino said the Government welcomed the deal finally being struck.

"Our firefighters make an enormous contribution to keeping our community safe. They deserve to be supported and respected with the security of a workplace agreement," he said.

"This industrial uncertainty has gone on for far too long."

Mr Merlino said for the first time fire services and the UFU had agreed to work together to tackle cultural and diversity issues.

Thursday's deal was struck just days after the UFU gave notice that it would appeal a Supreme Court decision made last year to allow the Victorian Equal Opportunity and Human Rights Commission to release a report into sexual discrimination, harassment and bullying in the state's fire services.

The commission had been preparing to release the report, which the UFU argued was improperly carried out. It also held suspicions about bias against it.

Shadow emergency services minister Brad Battin said the Andrews Government was morally corrupt and the deal was yet more evidence.

"Daniel Andrews' behaviour is more like a dictator than a Premier," Mr Battin said.