Administrator Mark Irving KC reportedly ditched two anti-corruption teams hired to uncover misconduct in the union as concerns were raised over the probe's investigative capacity, according to Nine newspapers.
The revelations prompted calls from the coalition for a parliamentary inquiry into the administration, which it claimed had avoided parliament and "proper scrutiny".
Employment Minister Amanda Rishworth dismissed the "absolutely baseless claims" in parliament on Monday, calling them a disgrace.
"(The coalition) ... might want to play politics with this issue," she said.
"We want to see a construction industry free from corruption. We are dedicated to the task, and we will work until that task is done."
The office of the CFMEU's administrator was contacted for comment.
Earlier, opposition employment spokesman Tim Wilson called on Mr Irving to face a parliamentary inquiry.
The union's construction division was forced into administration by the federal government in 2024, after allegations were made of bikie figures infiltrating the union and other criminal activity.
Liberal senator Maria Kovacic will on Tuesday move to set up an inquiry into the CFMEU's administration.
The bid will need the support of the Greens in addition to two other crossbenchers to get the numbers needed for a majority of senators.
Greens leader Larissa Waters said the party would wait to see the proposal before lending its support, but left the door open to an inquiry.
"As the revelations over the last few days have suggested, there's pretty broad issues going on in the building industry, and all of that misconduct from all quarters needs to be looked at properly," she said.
Senator Kovacic said the inquiry was an "absolutely necessary step" to understand what was taking place in the union's administration.
The High Court in June dismissed a case brought by the CFMEU which attempted to overturn the federal government's decision to place the union's construction division into administration.
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