The prime minister says the Australian Workers' Union and Bill Shorten have questions to answer, despite the union categorically denying destroying documents related to a watchdog investigation.
"The AWU should comply with the law," Malcolm Turnbull told reporters in the NSW town of Sutton on Wednesday.
"The AWU has got questions to answer, Bill Shorten has questions to answer."
Australian Federal Police simultaneously raided the union's Sydney and Melbourne offices on Tuesday to execute warrants as part of a Registered Organisations Commission investigation.
The watchdog is examining whether AWU donations - made 10 years ago - to activist group GetUp! when now federal Labor leader Mr Shorten was in charge were properly approved under union rules.
It is also examining a $25,000 donation to Mr Shorten's own campaign to enter federal parliament.
The ROC sought the warrants because it had "reasonable grounds" to believe documents related to its inquiry could be "concealed or destroyed".
Asked if any relevant documents had been destroyed union national secretary Dan Walton told the Nine Network: "Absolutely not."
"I think it is quite extraordinary, the claims that are being made."
Mr Shorten accused the coalition of a "grubby effort" to "damage the reputation of their opponents".
"The regulator, at the behest of the government, is conducting a political witch-hunt designed to throw mud in the hope that some will stick."
The AWU is expected to challenge the validity of the warrants authorising the AFP raids in the Federal Court in Melbourne on Wednesday.
Mr Walton said the AWU was already cooperating with the watchdog.
"This isn't a question of whether or not the donation was made," he said.
"This is a question of whether or not we filled in the paperwork correctly. And we ended up with 32 AFP police officers barging down the door."
Federal Employment Minister Michaelia Cash earlier this month referred the donations issue to the ROC following reports the AWU gave about $100,000 to the left-wing advocacy group in 2005.
Mr Walton branded the raids "an extraordinary abuse of police resources" and smear attempt.
"I'm quite comfortable to stand up here today to be able to say everything was above board," he said.
GetUp! on has 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.
Mr Turnbull asked why the AWU made a donation to Getup, "an organisation which I might say is opposed to most of the industries that employ members of the AWU".
The commission's website said its investigation into the AWU's national office and the Victorian branch commenced on October 20.
