Detectives from Taskforce Hawk, established to tackle criminal behaviour in the construction sector, executed warrants at six addresses on Monday morning.
They were conducted as part of an investigation into alleged fraud, drug trafficking and secret commissions, which can refer to corrupt, undisclosed financial benefits, rewards, payments or kickbacks, police said.
The force confirmed the CFMEU's headquarters, on Elizabeth Street in Melbourne's city centre, was raided, along with five residential addresses.
Five men, believed to be union organisers, were arrested.
Three of the men - a 27-year-old from Gisborne, a 56-year-old from Powelltown and a 37-year-old from Somerville - were released pending further enquiries.
A 36-year-old Chirnside Park man and a 46-year-old Westbury man were charged with a single drug and two firearms offences, respectively, and bailed to appear in court at a later date.
No arrests were made at the Elizabeth Street office, police said.
Detectives seized a number of items during the searches, including four CFMEU-registered vehicles, digital devices and documents.
The CFMEU's administrator said the union and its staff were co-operating with Victoria Police.
"Criminals and bad actors in construction remain a major threat to the workers which is why we need greater regulation and scrutiny across the sector," Michael Crosby said in a statement.
"This administration has undertaken unprecedented reform and anyone associated with criminal elements will have absolutely no place in this union's future."
The union would conduct its own investigations, the statement said
It comes after Victorian Premier Ben Carroll released the terms of reference for a royal commission into the state's construction sector.
It will investigate the extent to which corruption, criminal conduct or serious misconduct has occurred on or surrounding any major public and civil infrastructure projects.
That includes any such activity undertaken or instigated by the CFMEU, construction companies and consortia, sub-contractors, labour-hire companies, contractors, suppliers or others.
The commission can also investigate whether Victoria's executive government or delivery authorities adequately followed their roles and responsibilities.
Barrister Geoffrey Watson's Rotting from the Top report claimed organised crime infiltrated the union and estimated Victorian government inaction caused $15 billion in blowouts on the state's $100 billion Big Build program.
The inquiry is due to produce a final report in August 2027, but Mr Carroll said it could run longer.
"I think it will be an 18-month, potentially two-year process, but I don't want to pre-empt anything," he told Melbourne radio station 3AW on Monday morning.
The premier reiterated the commission would have the power to call him, former premiers, current ministers, business leaders and union bosses.
The construction and general division of the CFMEU was placed into administration in 2024 following allegations Victorian and NSW projects had been infiltrated by underworld figures and bikies.
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