Raids at the Australian Workers Union headquarters in Melbourne and Sydney are likely to see the union challenge the investigation and warrants in federal court.
The Australian Federal Police raided the headquarters on Tuesday in support of a Registered Organisations Commission investigation into donations the AWU made to activist group GetUp! when federal Labor leader Bill Shorten was in charge of the union.
Union lawyers are expected to challenge the investigation at Melbourne's federal court on Monday, an AWU spokesman told AAP.
"The application will be to object to the validity of the investigation and the warrants," the spokesman said.
The ROC received information that documents were being interfered with in the union's offices "by being concealed or destroyed" while it was investigating whether the donations were within the union's rules.
It said a magistrate authorised the AFP raids to seize the documents.
Employment Minister Michaelia Cash earlier this month referred the issue to the ROC following reports the union gave about $100,000 to the left-wing advocacy group when it launched in 2005.
AWU's national secretary Daniel Walton branded the raids "an extraordinary abuse of police resources" and were part of an attempt to smear Mr Shorten.
National secretary Daniel Walton said the documents seized were over 10 years old and "do nothing more than highlight the fact that the union made a few political donations".
"We're extremely concerned about the actions of the Registered Organisations Commission and extremely concerned of the actions of the Turnbull government," Mr Walton said on Tuesday.
GetUp! on Tuesday said it had previously acknowledged receipt of a donation of $100,000 in 2005 from the AWU.
"There is no suggestion of any impropriety on GetUp!'s part on the receipt and handling of the donation," a spokesman told AAP in a statement.
The commission's website says an ongoing investigation into the AWU's national office and the Victorian branch commenced on October 20.