Hoegh Autoliners specializes in transporting cars, controlling 50 specialized vessels or 6-7 percent of the global fleet in this market.
South Africa's Competition Commission said on Tuesday Hoegh Autoliners had been referred for prosecution on seven charges relating to collusive tendering, price fixing and market division.
Hoegh Autoliners "stands accused of colluding with a Japanese car shipping company, Mitsui O.S.K Lines Ltd (MOL)," the Commission said in a statement.
"From around 2009, MOL and Hoegh engaged in prohibited practices in that they agreed and/or engaged in concerted practices as competitors to fix prices, divide markets and tender collusively."
Hoegh Autoliners said it denied the allegations.
"We are not admitting any guilt and we will defend ourselves," Nyrud told Reuters, adding that a probe had been continuing since 2013 and that he was surprised by Tuesday's statement.
No one at Mitsui O.S.K Lines was immediately available for comment when contacted by Reuters.