After an emergency meeting on Monday, the union's national office will assume senior executive powers and set up an independent process to probe into the allegations of criminal behaviour.
It followed media reports outlaw motorcycle gangs were acting as CFMEU delegates and there were links between construction projects and organised crime groups.
CFMEU national secretary Zach Smith said the allegations were serious and demanded an unprecedented response.
"The CFMEU has zero tolerance for criminality and anyone found to have engaged in criminal conduct while representing the CFMEU will be identified and removed," Mr Smith said.
"The CFMEU has one purpose and one purpose only and that is to defend and advance the safety and conditions of workers."
ACTU secretary Sally McManus also condemned the alleged actions, saying there was no place for criminal activity within unions.
"Such people should face the full force of the law. The ACTU calls on the national leadership to stand down those subject to criminal allegations," she told reporters in Melbourne.
ACTU secretary Sally McManus called for those subject to criminal allegations to be stood down. (Joel Carrett/AAP PHOTOS)
"We want to see a functioning and strong and corruption-free union in the building industry."
The ACTU executives will meet on Wednesday to discuss the issue involving the construction union.
The federal government said all options, including deregistration of the CFMEU, were on the table in addressing the allegations.
Ms McManus said any move to deregister the union would depend on the CFMEU's actions in dealing with the situation.
"It's not just words and platitudes, there must be action," she said.
Prime Minister Anthony Albanese welcomed news of the branch being placed into administration.
"That's a good next step, but we need further action, and we need to make sure that that results in an isolation and both action in terms of the law but also action within the union," he told ABC Radio.
"I have a very clear message for the CFMEU, which is, they need to clean up their act. I have zero tolerance for it."
CFMEU boss John Setka stepped down from his role on Friday. (James Ross/AAP PHOTOS)
The head of the Victorian branch of the CFMEU John Setka quit on Friday night but not before describing the reports as "false accusations" and "malicious attacks".
The prime minister said the allegations raised were a betrayal of union members.
"If there are any breaches of the law, they need to be prosecuted to the fullest extent, and people need to be held to account," he said.
"I have contempt for someone like John Setka, he has no legitimate role in the union movement."
Mr Smith said while allegations of wrongdoing needed to be examined, union officials did not need to be smeared with the same brush.
"Cancel culture will never be our culture," he said.
"Our union operates in a tough industry in which people are badly hurt or killed every week and in which shonky developers and contractors are allowed to run rampant.
"The national office will be uncompromising in cleaning up whatever wrongdoing we find because we know that blue-collar workers depend on our union being strong and effective."
Shadow treasurer Angus Taylor called on the Labor government to stop taking donations from the CFMEU (Mick Tsikas/AAP PHOTOS)
Shadow treasurer Angus Taylor said the government, as the Labor Party, must stop taking donations from the union, deregister the CFMEU and re-establish the Australian Building and Construction Commission, which it abolished in 2023.
"Actions speak louder than words," he told Nine's Today program.
"And the Labor Party's been very close to the CFMEU."
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