A decision by the Supreme Court on the law related to penalties for failing to fully record fishing catches may affect up to 60 existing prosecutions.
However, the law has been amended since the case was brought by Spanish man, Juan Montemuino, and future prosecutions will not be affected by the court's decision.
The legislation governing fishing in Ireland was described by Supreme Court judge Mr Justice Frank Clarke as "complex and highly technical".
Mr Justice Adrian Hardiman said both Irish and EU fisheries laws "at times seem deliberately to court complexity and obscurity".
The court rejected a claim by Mr Montemuino that the law was unconstitutional.
But it also rejected arguments by the Minister for Marine and the State that the relevant section allowed the seizure of all the fish and fishing gear on an offending vessel.
The court ruled the relevant section meant a sentencing judge has discretion as to the amount of fish and fishing gear that should be forfeited.
In exercising that discretion, it was necessary to have regard to the importance of ensuring penalties were proportionate, it added.
Mr Montemuino was the master of an Irish fishing vessel, the Ocean Enterprise, which was registered in the port of Tralee, in 2005.
The vessel was owned by Patrick Brown and leased from him by Brendan Rogers.
Mr Montemuino was charged with failing to record a quantity of Greater Forkbeard, a non-quota fish species, valued at €600, after fisheries officers boarded the vessel in December 2005.
The value of the entire catch on board the vessel was more than €30,000.
Mr Montemuino's trial has remained on hold pending the outcome of his legal challenge.