The Maritime Union of Australia (MUA) will join other trade unions to help fund the CFMEU's legal battle, claiming the federal government's decision was "unjustified, chaotic and reckless".
Putting the construction union into administration had both short and long-term consequences, the maritime workers' group warned.
It could jeopardise progress on enterprise bargaining agreements, send a green light to "bad and abusive employers" or set a precedent for moves against other unions based on "untested media allegations".
"We are supporting ... and backing them in as they fight for the right of their division to exist," the Maritime Union of Australia said in a statement released on Thursday.
"We are also concerned by the near certainty that similar future legislation will be used by governments of either stripe against other militant blue-collar unions, including the MUA."
"We have been on the receiving end of these calculated political and media smears in the past and will support our fellow members ... as they seek to clear their names and fight for the principles of natural justice, presumption of innocence, the rules of evidence and procedural fairness."
Former Victorian CFMEU boss John Setka reportedly criticised the federal government while addressing union members at the Footscray Hospital construction site in Melbourne on Wednesday.
The embattled CFMEU had its construction and general divisions placed into administration after allegations of corruption and bikie infiltration prompted the federal government to try to rein it in.
Laws to bolster this effort passed Parliament in August and gave the relevant minister powers to intervene and slap life bans on CFMEU officials.
Mark Irving was soon appointed as administrator and more than 200 elected CFMEU officers were immediately terminated.
For weeks, the construction union indicated it would fight the legal battle and on Tuesday, it launched its challenge in the High Court.
The administration period could last up to five years.
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