SGE Credit Union says it wasn't one of the businesses raided by fraud squads as part of investigations into the Health Services Union (HSU) East branch.
Victoria police confirmed they had searched a number of premises in Sydney on Thursday, but would not say which businesses had been targeted.
"As the investigation is ongoing it's not appropriate to comment any further," a spokeswoman told AAP on Friday.
It has been widely reported that SGE Credit Union - where HSU president Michael Williamson and national secretary Kathy Jackson have been board members - was among those raided.
But the credit union issued a statement on Friday denying the reports.
"SGE Credit Union's offices have not been raided," it said.
"Several media outlets (have) published false and irresponsible reports about SGE Credit Union."
The company's CEO, Dave Taylor, described the reports as "completely untrue".
"We've contacted those media outlets and made absolutely clear to them, there is no raid, there's been no search, there's been no search warrant," he told AAP.
The raids came three days after Fair Work Australia released a report alleging embattled MP and former HSU boss Craig Thomson spent as much as $500,000 of union funds on electioneering, escort services, lavish meals and cash withdrawals.
Other investigation findings relate to Ms Jackson and Mr Williamson.
The report found multiple failings regarding the union's financial controls, including a lack of rules governing credit card use, no proper auditing and officials' wages being set without checks by the union's national bodies.