The Serious Fraud Office says it is looking into a complaint made about the financial records of the Meat Workers' Union.
The complaint has been laid by meat processing company AFFCO, which has locked about 800 workers out following a breakdown in negotiations over a new collective employment contract. A further 500 workers are on strike.
Mediation between the company and the union is planned for Thursday.
AFFCO chief executive Hamish Simson says the union's financial statements show only a fraction of the union fees the company deducts and passes on from workers' wages.
Mr Simson says AFFCO's workers pay $500,000 a year to the union at $5.95 a week each. The workers represent about 10% of the union's members, but the union has only declared a total income of $700,000 a year.
But the Meat Workers' Union on Wednesday dismissed the fraud complaint as unfounded.
National secretary Dave Eastlake says AFFCO's claim it has not declared all of its income from members' fees is incorrect.
"It hasn't taken into account that the Meat Workers' Union's made up of four independent branches that collect the union fees off the members.
"They run autonomous accounts and have them audited and pay a capitation to the national office. All the complaint is about is the national office accounts."
Mr Eastlake says AFFCO's complaint is an attempt to divert attention from the mediation session.
The Serious Fraud Office on Wednesday confirmed that a complaint about the Meat Workers' Union has been made and it will evaluate the matter by mid-May.