Legislation giving the minister power to appoint an administrator passed the Senate on Monday and is set to be ticked off in the lower house as early as Tuesday.
Workplace Relations Minister Murray Watt said an administration scheme would be in place "over the next week" as the government pounced on allegations of corruption and bikie infiltration.
"I would completely disagree that this is an attack on construction workers, quite the opposite," he told ABC News on Tuesday.
"Construction workers deserve to have a strong and effective union, but it's got to be a clean union."
The union criticised the law, saying it stripped members of the right to a fair process.
Criminal allegations were taken seriously and people had been stood down pending legal proceedings but they remained untested in court, CFMEU national secretary Zach Smith said.
"Until allegations have been tested by the legal system, people and organisations are entitled to a fair process," he said.
"The deal cut by Labor and the coalition is as shameful as it is unnecessary – an act of political expediency at the expense of fundamental tenets of Australian democracy and our legal system."
The union could challenge the bill in court.
The opposition agreed to pass the bill after securing several amendments, including a three-year minimum administration period for the union and its branches that only the administrator could end early.
Senator Watt took aim at the Greens for not supporting the amendments.
"The Greens party were the only party in the parliament that decided to side with John Setka and the organised crime and bikie elements around the CFMEU rather than taking this side of the Australian people," he said.
The Greens have criticised the deal, but business and building groups welcomed the move.
Greens leader Adam Bandt said if the coalition won the next federal election, they could bring former prime minister Tony Abbott in to administer the union.
"What Labor and the anti-worker Liberals have done is rush through legislation that is an unprecedented attack on the rule of law," he told reporters in Canberra.
The administration period can last up to five years under the law and officials found guilty of crimes would be banned for life and unable to become bargaining agents at other registered organisations without holding a fit-and-proper-person certificate.
Those who attempt to frustrate or obstruct the process could face hefty fines and two years' prison.
The administrator has assured the opposition the union would not spend money on political campaigns or donate during the takeover.
"That is possibly the most significant part of what we wanted," opposition workplace relations spokeswoman Michaelia Cash said.
Social Services Minister Amanda Rishworth said the intervention was the strongest possible action that can be taken to "stamp out some of this really horrific behaviour".
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