An SFO spokeswoman had earlier said the complaint would go through a 20-day evaluation period.
Meat workers union national secretary Dave Eastlake said the SFO complaint was a "publicity stunt complaint that has already be found to be without substance to detract attention from their brutal lock out of Affco workers and families".
The New Zealand Institute of Chartered Accountants had already investigated a similar complaint and advised no action would be taken, Eastlake said.
He said the complaint was an attempt from Affco's owners Talley's to gain extra leverage in an ongoing industrial dispute.
"It is disingenuous for Talley's Affco to try and suggest there is money missing from the union's national account when they know we audit our four branches separately from our national account, which is a common legal practice," he said.
"We are concerned, but not surprised, that Talley's Affco chose to start their latest smear campaign the day before we go to mediation."
Eastlake said the union's accounts were audited and available to members.
"It's a load of rubbish.
"You can't hide things when you've got 20,000 members that can see what you're doing. You don't last long even if you have an extra cup of coffee."