Commission spokesperson Themba Mathebula confirmed to the newspaper that the case involving Sekunjalo's Premier Fishing had been referred to the commission's tribunal for final adjudication.
"The case is now at our legal services department and they are finalising the referral process."
This most recent development followed a long investigation into claims that fishing companies were colluding to charge set prices for skippers, crew, and private boat owners.
Sekunjalo spokesperson Cherie Hendricks told the newspaper that Premier Fishing acted with "a good governance standard".
"We are confident of our position as we have communicated this to the commission," she said.
The newspaper reported that in Sekunjalo's annual report, released towards the end of last year, it had made provision for an "expected penalty...The settlement terms are currently being negotiated".
Another company, Oceana fishing, has already paid a R35m fine in connection with the investigation.