CFA chief fire officer Joe Buffone is the latest scalp in the bitter Victorian firefighters pay deal dispute.
Mr Buffone's resignation comes after the Andrews government sacked the CFA board earlier this month because it repeatedly refused to back the enterprise agreement with the organisation's professional firefighters.
The board cited concerns it handed too much power to the United Firefighters Union.
The CFA's chief executive officer, Lucinda Nolan, subsequently quit and Mr Buffone temporarily filled her role until Frances Diver took over the position earlier this week.
Former Emergency Services Minister Jane Garrett had been the first to be ousted in the saga.
She resigned from the Labor cabinet on June 10 rather than support the union deal and James Merlino took over her portfolio.
He issued a statement on Thursday suggesting Mr Buffone had resigned due to concerns over his own pay rather than the EBA.
Mr Buffone had resigned on Tuesday but then offered, through lawyers, to stay on if he had equal status and salary with the chief executive - an $85,000 upgrade, the minister told reporters.
Mr Buffone said his resignation was due to concerns about the EBA, not about his pay.
Union secretary Peter Marshall on Thursday was asked if he was "collecting scalps".
"The only thing I am collecting is good will," he told reporters.
He says there's been a campaign to divide career and volunteer firefighters, to help the Liberal Party win votes in the federal election.
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