Bosses are being urged by the nation's workplace umpire to dob in any employees who walked off the job in support of the CFMEU.
Thousands of workers marched in capital cities across the country on Tuesday after hundreds of CFMEU officials were sacked last week when Attorney-General Mark Dreyfus placed its construction and general divisions into administration.
Eureka flags, known as a symbol of defiance and collective action, were waved by angry protesters who wore high vis gear to the rallies.
Workers face tough penalties due to the unprotected action, with the Fair Work Ombudsman warning that those who failed to turn up or walked off the job without permission could be in breach of workplace laws.
Employers are legally required to deduct four hours pay for people who show up to unprotected action, even if they were gone for less than that time.
"After national rallies today, employers are encouraged to notify the Fair Work Ombudsman of any potential unlawful industrial action at their workplace," the ombudsman said.
A spokesperson for the CFMEU administrator said the union was no longer involved in the planning of the protest and reiterated "the taking of unprotected industrial action is not lawful".
Electrical Trades Union state secretary Peter Ong told a rally in Brisbane the administration laws were an attack on the trade union movement.
"This is the union, comrades," referring to the crowd.
"This is not an attack on the CFMEU, this is an attack on the trade union movement…from what we thought was our own."
Rally organiser Jade Ingham also likened the law to the "greatest attack on Australian democracy".
"This act of treachery, this act of class warfare that was committed on the trade union movement by the Labor Party will not be forgotten," he said.
"(Our members are) emotional, angry, shocked ... they're upset that their democratic rights have been taken from them."
Prime Minister Anthony Albanese said while there would be consequences for those taking part in unprotected industrial action, the union needed to be cleaned up.
"Trade unionists know that their unions do a good job free of corruption, and they do a good job making sure that the wages and conditions of working people are looked after," he told reporters in Sydney.
"What we want to do, though, is to make sure that their union is free of corruption. That is in the interests of all trade unionists."
Treasurer Jim Chalmers said blowback was expected to the move against hundreds of union officials.
"Our goal here is to clean up the CFMEU to get it back to representing its members and workers in a really important part of our economy," he told ABC Radio on Tuesday.
Opposition workplace relations spokeswoman Michaelia Cash blamed the government's handling of the situation after scrapping the construction sector watchdog.
Labor abolished the Australian Building and Construction Commission, arguing it was ineffective, with alleged offences happening under its watch.
NSW Premier Chris Minns said having administrators at the helm of the union meant the "bad eggs (were) absolutely" gone
"There might be a last gasp today, but nothing will change, and it's important that the new leadership of the CFMEU are put into place," he told Sydney radio station 2GB.
The Electrical Trades Union (ETU) and maritime union backed the protest and urged their members to join rallies.
The ETU slammed the treatment of the union in comparison to companies that weren't placed into administration following royal commissions into banking and aged care.
"The CFMEU on the other hand - one of Australia's strongest unions, is now forced straight into administration on the back of a handful of rumours and allegations," it said in a social media post.
The old leadership of the CFMEU had flagged a legal challenge of the takeover, saying members were denied due process and their democratic rights.
