Health Services Union head Michael Williamson was stopped allegedly trying to remove documents as police raided his Sydney offices this morning.
Mr Williamson was stopped in the car park of the union's East branch building in Pitt Street, Sydney.
Detective Superintendent Col Dyson, Commander of the NSW Fraud and Cybercrime Squad, said that any interference may result in criminal charges.
Up to 10 police officers raided the building to examine computers and seize documents.
The building has been shut down and the union's national secretary Kathy Jackson, who arrived at 9.30am, has been unable to get in.
Mr Dyson said there was no political consideration in the timing of today's raid and police had briefed no-one from the federal government.
He said the police investigation was completely independent from any other and police were already in possession of the interim report by Ian Temby, QC, and auditor Dennis Robertson, which found that millions of dollars had been paid to suppliers to the union, with no tenders, no price guidelines and no probity checks. Some of those companies were associated with Mr Williamson and his family.
Ms Jackson, who is also executive president of HSU East branch, said she expected the information taken in the raid would uncover corrupt behaviour.
She also agreed with suggestions that HSU executives had created their own fiefdom and engaged in free-for-all business practices.
"I have no doubt that the police will uncover documents that will prove that," Ms Jackson told reporters outside the HSU East premises.
She said the raid was "a long time coming" and a sad day for "the organisation that needs cleaning up".
Ms Jackson dismissed speculation the raid was planned after Prime Minister Julia Gillard dumped former HSU boss turned federal MP Craig Thomson from the Labor Party last week.
"I think that's just about all of the government realising that D-Day was coming and they had to act," she said.
"The perfect time would have been if she had acted eight months ago."
Investigators from State Crime Command's Fraud and Cybercrime Squad executed a search warrant as part of the investigation.
Strike Force Carnarvon was established in September last year after allegations raised by the Herald that Mr Williamson and Mr Thomson had received secret commissions from a major supplier to the union.
Two months ago, officers from the same strike force searched a house in Sydney's northern beaches. It is believed to be the home of graphic designer John Gilleland, who runs a printing business and allegedly provided credit cards to Mr Thomson and Mr Williamson.
Police are expected to spend most of the day at the union offices.
Mr Williamson is on paid leave from the union while Mr Thomson was suspended from the Labor Party earlier this week pending the outcome of investigations.
It has separately been alleged Mr Thomson misused a union credit card for prostitutes, lavish meals and cash withdrawals when he was the HSU's national secretary between 2002 and 2007.
- with AAP