Fishing industry representatives have expressed surprise at yesterday's searches by up to 120 gardaí in four fishing ports in counties Kerry, Cork, Galway and Donegal.
Gardaí from the National Bureau of Criminal Investigation (NBCI) and local officers undertook a number of searches simultaneously yesterday morning in Castletownbere, Co Cork; Dingle, Co Kerry; Rossaveal, Co Galway; and Killybegs, Co Donegal.
Vessels, fish processing and exporting premises and private homes of skippers and owners were visited under warrant, and the Garda Press Office said that they "formed part of an investigation into alleged irregularities in the fishing industry".
However, the office was unable to confirm the legislation under which the searches took place, nor could it comment on the purpose of the investigation.
The new Criminal Justice Act, which has just been signed into law, and the controversial Sea Fisheries and Maritime Jurisdiction Act, which was the subject of protests last year, have sought to tighten up Ireland's fisheries control regime in an effort to appease the European Commission.
A new sea fisheries protection authority has also been established, with headquarters in Clonakilty, Co Cork.
However, the inclusion of the fishing industry in the Criminal Justice Bill by the former minister for justice, Michael McDowell, attracted criticism from the Federation of Irish Fishermen (FIF), which said that it was amazed that fishermen should be ranked in the same league as drug smugglers and violent criminals.
Sean O'Donoghue, chairman of the federation, said he was "surprised" at the searches as he believed that a new improved relationship between the Government and industry had been initiated under Minister for Agriculture and Fisheries Mary Coughlan.
Lorcan Ó Cinnéide, of the Irish Fish Producers' Organisation (IFPO), said the objective of the exercise was not clear and it was "slightly ironic that it should take place when some €200 million of illegal substance had been found floating off the southwest coast earlier this week".
It is understood that the investigation is separate to that initiated following complaints by Killybegs fisherman Pat Cannon to the European Commission.
A spokesman for Ms Coughlan said that she had no comment to make as it was a matter for the Garda Síochána.