Revenue officials, gardaí and other agencies have raided fishing vessels in Dublin and Cork as part of an investigation targeting undocumented workers.
The operation remains ongoing and so authorities have declined to comment on the details or whether any arrests have yet been made.
It is understood boats have been targeted in Howth, Co Dublin and Castletownbere, Co Cork.
There was significant Garda activity at Howth station on Wednesday morning but the nature of the operation remains confidential. It is expected to remain ongoing until later in the evening or into Thursday morning.
Ken Fleming of the International Transport Workers Federation (ITWF) said the raids had come following months of work to expose the practices within the industry.
Last February, the State made 500 special permits available for non-EU citizens to work in the Irish fishing industry but to date only 159 had been applied for. Mr Fleming said he estimated there are in the region of 1,000 foreign workers employed in Ireland.
“We have been beating the drum for everyone to step up to the plate and enforce the permit system and it has been very slow,” Mr Fleming said.
The ITWF has had inspectors visiting ports since the beginning of the year in an effort to gather evidence. Their sole concern is the treatment of crew members who are not legally employed, primarily from the Philippines, Egypt and Ghana.
Mr Flemming said those with permits would earn about €22,000 and endure severe conditions and long hours.
However, he said, there is non-compliance “throughout the whole country, in every port”.
Fingal Co Councillor Cian O'Callaghan, who represents the Howth area, said: "There would be a lot of concern in the wider community about undocumented workers in the fishing industry. Anything gardai can do about labour standards is welcome."
The Irish fishing fleet has shrunk in size in recent years and many of the jobs on boats are now taken by non-Irish and often non-EU workers.
In Howth, members of the fishing community say that during the Celtic Tiger period, many Irish crew members went ashore where they opted for work in the lucrative construction sector, leaving vacancies in crews.
Initially these were filled by immigrant workers from eastern Europe and in more recent times, say those in the industry, from farther afield.
While the industry was almost entirely locally run in the late 1990s, many Howth based boats were decommissioned during the mid-2000s and have been replace by fewer, more modern boats from other parts of Ireland.
Last year, the Guardian reported the Irish authorities had been aware of the trafficking of migrant workers into its fishing fleet as long ago as 2010 but failed to tackle the problem.
It cited documents obtained under Freedom of Information requests which purported to show trafficking of fishermen from countries outside the EU was raised by officials tasked with investigating illegal employment and the flouting of immigration laws in the sector.
An earlier investigation by the newspaper uncovered what is said were allegations of “widespread exploitation of undocumented Africans and Asians and suspected cases of human trafficking in the Irish prawn and whitefish fleet”.