The findings were detailed in the Independent Broad-based Anti-corruption Commission's Operation Richmond special report, tabled in Victorian parliament on Wednesday.
The probe examined the Andrews government's negotiations over enterprise bargaining agreements with the United Firefighters Union between 2016 and 2019.
It began in November 2018 following claims the union's secretary Peter Marshall blackmailed or compromised former Labor premier Daniel Andrews to change his position on the Country Fire Authority's enterprise bargaining agreement.
Mr Andrews and Mr Marshall insisted they had been vindicated by the report.
"These claims were baseless when they were made almost a decade ago and they remain baseless today," Mr Andrews said in a statement.
"For the record and the avoidance of any doubt, there are no findings in relation to corrupt conduct made about me, any other member of the government, or the public service."
Mr Marshall came out swinging against the corruption watchdog and declared his dealings with the Labor government were above board and standard practice.
"There is nothing wrong with what we've done, absolutely nothing," he told reporters.
However, the sweeping probe found senior officials and public servants acted contrary to government policies, procedures and conventions, increasing the risk of corrupt conduct.
"While IBAC did not find that any individuals engaged in corrupt conduct as defined in the IBAC Act, IBAC did find serious and concerning conduct by senior public officers," it said.
Commissioner Victoria Elliot stressed the findings were significant and raised integrity concerns.
"Victorians expect their elected officials to act honestly for the best interest of our state, without fear or influence," she said on Wednesday.
"Operation Richmond revealed a number of actions that do not meet that expectation."
The CFA pay deal became a major political headache for the Andrews government, culminating in the resignation of the late Jane Garrett as emergency services minister.
Ms Garrett's family issued a statement, saying she was under enormous pressure during the stressful time she was a minister.
"In her evidence, Jane said ahead of the ERSC meeting she refused to co-sign the cabinet submission because she could not in good conscience endorse an agreement which was opposed to what she swore in her ministerial oath – to act in the interests of the Victorian people and good governance," the statement read.
The Operation Richmond investigation exposed backroom dealings between Mr Marshall and public officials in the lead up to the deal.
Over four days in 2016, Mr Marshall engaged in undisclosed negotiations with former special minister of state Gavin Jennings, with the help of the premier's department secretary Tony Bates.
Authorised by Mr Andrews, those meetings occurred in rented meeting spaces and a hotel without the knowledge of Ms Garrett, the CFA or government agencies.
IBAC found those involved in the meetings were instructed to keep them confidential and concluded with a handshake deal, the terms of which were later presented to cabinet as a "UFU proposal", without word of the prior negotiations.
The watchdog claimed the secret deal weakened the government's bargaining position and Mr Marshall pressured the government to honour the agreement.
IBAC also found Mr Marshall, who later fought to prevent the IBAC report from being published, was given privileged access to senior ministers not available to other stakeholders.
The report has reignited debate about Victoria's corruption scheme, with an integrity body arguing the state's legal definition was too strict to capture all relevant behaviours.
"In most other anti-corruption commissions in Australia, this could form the basis for a finding of statutory corrupt conduct," the Centre for Public Integrity said in a statement.
Opposition Leader Jess Wilson said the report demonstrated a pattern of corrupt favouritism by the state Labor government.
IBAC made three recommendations, including to strengthen integrity standards for ministers, introduce a ministerial handbook and improve training on minister's obligations.
Mr Carroll, who has served in the cabinet since 2017, confirmed Mr Bates had taken a leave of absence and committed to implementing the report's recommendations.
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