The Federation of Irish Fishermen says the majority of fishermen are working for very little pay because fisheries regulations are forcing the dumping of fish catches at sea.
New FIF chairman Michael Walsh has called for an urgent meeting with the Minister for Agriculture, Fisheries & Food.
He says uncertainty in the industry is a serious threat to employment in many fishing ports.
Rigorous inspections by the Sea Fisheries Authority have led to several confiscations of fish catches in the past few weeks.
The authority has denied it is being heavy-handed and says it wants to ensure compliance with a vast array of EU regulations.
The FIF says it does not want the laws broken but, speaking after a meeting in Cork, Mr Walsh said fishermen were frustrated at having to dump good fish back in the sea.
While fishing for one species another could enter nets and if landed without a quota, fishermen could wind up with a criminal record for life.
This problem and the lack of a clear indication that the Government is going to financially support the Cawley Report to remove boats and fishermen from the industry was very serious for coastal communities where many fishermen were now working for very little pay.
The industry is in a very difficult and worrying situation, Mr Walsh said.
Read a statement from FIF Chairman Michael Walsh on the problems in the fishing industry and listen to an interview with him on RTÉ Radio's Seascapes programme here.
