Serious allegations of fraud, falsification of documents, and breaches of quotas by fishing vessels operating out of Killybegs in Donegal are to be investigated by the gardaí.
RTÉ News understands that it is also alleged that department officials colluded in illegal activity.
The allegations were made by an individual based in Donegal with a long-standing involvement in the fishing industry.
The Cabinet was briefed on the matter by the Minister for Communications, Marine and Natural Resources, Noel Dempsey, this morning.
It is understood it is being taken very seriously by the Government, both because of the nature of the allegations against department officials, and because of the possibility of EU action if the allegations are proven.
However, it is also understood that the individual making the allegations has a long-standing grievance against the department, and that while he showed documents purporting to back up his claim to officials during a meeting, he did not allow them to photocopy the documents.
It is likely that he will be required to hand over any documentary evidence to the garda investigation.
It is believed the allegations were first made in a letter to the department in July, and repeated in two meetings with officials in September.
The documents which were shown to the officials included log sheets and invoices for the sale of fish, but they could not be verified.
At the beginning of this month, the allegations were repeated in a letter sent to the Fisheries Commissioner, the Advocate General of the Court of Justice, and Fisheries Ministers in Britain, Portugal, Spain, France, Sweden, the Netherlands, Poland, Germany, Denmark, Belgium, Italy and Norway.