Representatives of the fishing industry warned the Government in 2008 that non-EU workers were being exploited by some skippers, they have claimed.
The Irish Fish Producers Organisation (IFPO) said it wrote to then-Employment Minister Micheál Martin to call for the proper monitoring of workers in the industry.
Chief executive Francis O'Donnell said he also wrote to current Jobs Minister Richard Bruton last month over concerns for workers.
The claim comes as gardaí told the Irish Independent that specialist officers have been investigating allegations of trafficking of workers since June.
A support group for workers says it is dealing with 17 cases where fishermen from outside the EU claim they were exploited and two other cases involving fishermen who claim they were trafficked into Ireland.
Mr O'Donnell, speaking in the fishing port of Killybegs in Co Donegal, said the industry had been expressing its concerns for years but that ministers had failed to respond.
A Fianna Fáil spokesperson said that as minister Micheál Martin had set up the National Employment Rights Authority (NERA) and secured the appointment of up to 100 inspectors to ensure that employers adhere to relevant guidelines.
"These inspectors did on the spot inspections of work places and employers were fined if they did not pay correct rates to workers," he said, adding: "NERA's remit included seafarers."
"Any report of incorrect salary rates would normally be examined and followed up to ensure it was corrected. Unfortunately, Fine Gael and Labour in Government decided to abolish NERA as a standalone agency, folding it and a number of other bodies into the WRC (Workplace Relations Commission)."
Mr O'Donnell rejected claims by Mr Bruton that there wasn't a need for a work permit system in the industry.
"As Irish people we all know too well that we have been exploited working abroad for generations, so as Irish people we don't want to see this happening in our country to people from other countries.
"The fact is that we struggle to get young Irish people involved in a fishing career and there is a need for work permits for non-EU workers in our industry. We have to stop the exploitation of people in our industry and we can do that by making sure everyone is fully documented."
He spoke out after a report in 'The Guardian' newspaper alleged widespread exploitation of workers from outside the EU.
He agreed with Grainne O'Toole from the Migrant Rights Centre Ireland that efforts should be made to legalise the workers.
"There is no point in having a crackdown and sending these workers home because they are the ones who will lose out on unpaid wages and their livelihoods," said Ms O'Toole.
However, Mr Bruton said he will not issue work permits for non-EU workers, claiming they were contractors because of payments including shares of catches.
"We give permits to areas where there is a proven skills shortage, where the employer has proven that he can't recruit people within Europe," said Mr Bruton.
However, Mr O'Donnell said many workers could be given contracts of employment due to the lack of recruitment inside the EU. "There is a legal method which this government can use to protect these workers and they are refusing to do it, and that's quite incredible" he said.