Opposition claims that the Criminal Justice Bill was criminalising commercial fishermen were rejected by Minister for Justice Michael McDowell.
He said that the provision in the Bill was purely to give fisheries protection officers the right to search premises.
"If they do not weed out the tiny minority who are betraying the great majority, we will have worse consequences next year. More boats will be tied up and the cycle will be repeated."
He said that the measure was no more an insult to fishermen than the inclusion of the Garda management board, which was also in the Bill, was an insult to gardaí.
He said that bearing in mind the urgency of making the fisheries protection law effective, and to stop another catastrophe whereby a "few traitors" could destroy fishing prospects for another season, the Minister for the Marine Noel Dempsey had asked him to include the provision in the Bill.
Sinn Féin spokesman Aengus Ó Snodaigh said he did not think there were "traitors" involved. "It has more to do with the foreign invaders that we have less fish stocks than before." He said the Bill gave significant additional powers to fishery protection officers and the Garda.
"I agree we need to regulate the fishing industry and ensure those involved do not break the law. However, to equate a person who has exceeded his or her fishing quota with a person who brings into this country €500,000 or €1 million worth of drugs, or who has shot innocent bystanders, is stretching things a bit."
Dinny McGinley (FG, Donegal South-West) said he was born and reared in a fishing port and he continued to live there.
"When I was much younger, some 30 or 40 half-decker boats left the port of Bunbeg. One would not see the two boats leaving that port nowadays."
Mr McGinley said he was amazed that the Criminal Justice Bill sought to lump in fishermen with big criminals and drug barons. "They have suffered so much in the past. There have been many tragedies at sea in Donegal, along the western coast and in many other European countries.
"They are on their knees at the moment."
Fine Gael spokesman Jim O'Keeffe said the Bill had been trumpeted by the Minister as his answer to gangland crime. "It is extraordinary that in the middle of it are proposals to further criminalise those involved in the fishing industry.
They resent the juxtaposition that arises from their being associated with gangland crime and they have a point."
Labour spokesman Brendan Howlin said the Bill was a most inappropriate vehicle to deal with changes in maritime law.
"It is insulting to the fishing industry which is already on its knees.
"Communities like Kilmore in my constituency are reeling from the pressures of a declining income from fisheries."
Debate on the Bill continues after the Easter recess.
