CFA chief fire officer Joe Buffone is believed to be on a collision course with the government over concerns the deal - rubber-stamped by cabinet earlier this month - would make it difficult or impossible for him to fulfil his legal obligations.

Mr Buffone, who was appointed chief officer by the Andrews government in October, has expressed concerns that he will no longer be able exercise his powers under the CFA Act, despite retaining legally responsibility for enforcing it.

The Act makes clear that all brigades, officers and firefighters fall under the chief fire officers' command. It also details a raft of other powers and responsibilities for the chief fire officer, including inspecting brigades, ensuring equipment is in working order, assessing and investigating firefighting operations and entering buildings.

But the CFA has expressed concern those powers could be at odds with a proposed clauses requiring union agreement for CFA operational and management decisions.

Former CFA chairman John Peberdy said the clause requiring union agreement - referred to by many as a veto power - would cause particular frustration, particularly since it is up to the chief fire officer to make often complex decisions about clothing and equipment.

These decisions could potentially be overturned or delayed by the union, Mr Peberdy said.

"The more practical element is that day-to-day decision making can be challenged and overturned," he told Fairfax Media.

At this stage, it remains unclear whether Mr Buffone will retain his position, with the government insisting the organisation must now work to implement the deal.

The dispute has already resulted in the resignation of Jane Garrett as emergency services minister, the resignation of Lucinda Nolan as CFA chief executive, the sacking of the entire CFA board and the appointment of a new board.

A spokeswoman for new Emergency Services Minister James Merlino said the government had confidence in Mr Buffone as chief fire officer and in the CFA board's "ability to finalise the EBA and deliver the cultural change the organisation needs".

"As the CFA board has made clear, there will be a period of consultation on the Enterprise Agreement before it is put to a vote of the CFA workforce," the spokeswoman said.

The pressure on Mr Buffone comes as a leaked email from a CFA operations manager to staff shows that the organisation is distancing itself from fact sheets and a website launched by the Andrews government to set the record straight on the controversial EBA.

In the email the senior official says to staff "please do not use this fact sheet nor refer anyone onto the website. It is not endorsed CFA position, and the Chief (Mr Buffone) is aware".

The CFA said the website could not be endorsed because the agreement with the United Firefighters Union was not signed off and consultation was continuing with volunteers, so it was not possible to have official information yet.

It came as United Firefighters Union secretary Peter Marshall launched a new federal election ad attacking the Liberals using the CFA crisis to raise cash.

The website Hands off the CFA was registered on April 28, well before the crisis became a full fire storm for the Andrews government – some people who signed the online petition were then sent emails trying to solicit donations for the Liberal Party.

The website has no Liberal logo but does have the authorisation of Liberal state director Simon Frost.

"The Liberals have manipulated fears about false changes to fabricate a federal election issue, and promised actions the legal experts now say may not even be deliverable," Mr Marshall said.