Up to 50,000 workers marched in Melbourne and thousands more went out in Sydney, Brisbane and other regional capitals, ignoring threats their pay could be docked by taking the unprotected action.
Union bosses across the country vowed to fight the administration, branding the Labor government a traitor to the labour movement.
The Electrical Trades Union has threatened to withhold $1 million from Labor ahead of the election. (Joel Carrett/AAP PHOTOS)
Unions have flagged a willingness to fund legal challenges.
The Electrical Trades Union is set to withhold $1 million from Labor ahead of the federal election and use the funds to back a court fight.
Professor John Flood says it's unlikely to succeed as the process is "perfectly legitimate".
"The Fair Work Commission needs to be able to handle an organisation that isn't running in the best interest of its members," he told AAP.
He pointed to the Health Services Union being placed into administration in 2012, saying it was "cleaned up and now it's running quite well" as an example.
Workplace Relations Minister Murray Watt, who oversaw the passing of the laws allowing for administration, said they were written to withstand a legal challenge.
"We have absolutely expected that the CFMEU, and potentially other unions, would seek to challenge the legislation," he told ABC radio on Wednesday.
Murray Watt says most union members recognise the damage CFMEU has done to the labour movement. (Dean Lewins/AAP PHOTOS)
The Greens have drawn scorn from the government for attending the protests in support of the CFMEU as the minor party argued it was standing for the principle of a fair trial.
Outspoken MP Max Chandler-Mather said due process had been abandoned and people had a presumption of innocence before the court.
But Prof Flood disagreed, saying the Fair Work Commission wasn't "an investigator, judge and jury" but needed the power to look into the serious allegations.
"Prosecuting through the court would then be done in the proper way," he said.
Labor is also targeting Chandler-Mather for what they labelled grandstanding and political opportunism.
"The most dangerous place you can possibly be is between Max Chandler-Mather and a TV camera," Senator Watt said.
Federal Greens MP Max Chandler-Mather has defended his attendance after being attacked by Labor. (Jono Searle/AAP PHOTOS)
"It's all about trying to get his profile up."
Finance Minister Katy Gallagher said he had to explain why he thought it appropriate to speak at a rally amid serious allegations of violence, intimidation and misogyny within the union.
Mr Chandler-Mather defended himself, saying while the Greens "are appalled by allegations of corruption and misogyny", a dangerous precedent had been set.
"I spoke at the rally in support of the tens of thousands of construction workers, 99.9 per cent of whom have faced no allegations of wrongdoing," he said.
"Yet they have all been deprived of their basic right to a democratic, independent union and natural justice."
The Greens' refusal to back the administration laws or rule out receiving donations from the CFMEU has also sparked anger within the government as the minor party targets Labor seats.
The biggest protest happened in Melbourne where about 50,000 CFMEU backers took to the streets. (Joel Carrett/AAP PHOTOS)
Asked about the impact on Labor's election war chest, Senator Gallagher said it wasn't about the donations for the party but about "what's the right response to serious allegations about violence, intimidation and misogyny in a union".
Mr Watt defended the government's standing within the labour movement, saying the vast majority of unions and members didn't march.
"They recognise the damage that has been done to the union movement through the constant unlawful and criminal behaviour that unfortunately has penetrated the CFMEU," he said.
