The Melilla 201 and Melilla 203 were investigated by the ministry in December 2007 for area misreporting - an offence in which fish are caught in one area but declared as coming from another.
The ministry found about 745 tonnes of fish on both vessels was misreported from eight voyages in 2007.
Ministry of Fisheries senior fisheries investigator Geoff Backhouse, of Wellington, said the vessels were owned by Korean company Dae Hyun Fisheries Ltd and were chartered by New Zealand company Trans Pacific Fishing Ltd.
The captains and crew of both vessels, and Dae Hyun's New Zealand representative were fined $360,000 and had to pay a $300,000 redemption fee to get their boats back.
Mr Backhouse said Trans Pacific's fight for the $900,000 worth of fish products continues in the Wellington District Court.
"It's the biggest area misreporting case the ministry has investigated to date."
Dae Hyun went into liquidation soon after the seizing and the vessels were bought by another Korean fisheries company - Haemin Corporation Ltd.
Haemin has managed to obtain another fishing charter in the south seas for the Melilla 201 - with United Fisheries in Christchurch.
However, the company was unable to obtain a charter for the Melilla 203, so it had been berthed at the X/Y sheds in Otago Harbour since May last year, Mr Backhouse said.
New Zealand representative for Haemin Chris Ludeke could not be contacted yesterday to comment on the future of the vessel.
A Port Otago spokeswoman declined to comment on how much it was costing the company to keep the vessel berthed at the X/Y sheds, saying it was commercially sensitive information.
