The accusations being investigated by the Garda Commissioner centre on the fraudulent falsification of logbooks on Killybegs trawlers.
Speaking to the Irish Examiner last night Mr Dempsey said the allegations were so serious they had already been forwarded to the gardaí for investigation.
"I have asked the gardaí to investigate and I take the allegations very seriously," he said.
The allegations, which involve logbooks for at least two Killybegs trawlers being altered to under-represent catches, first surfaced in July when a former skipper on both boats wrote to the department and the Killybegs Fishermen's Organisation (KFO).
In several subsequent meetings with department officials in September, the individual concerned claimed to have evidence of widespread corruption, facilitated by fisheries officers.
However, department officials were only allowed access to the logbooks and related invoices for a brief period during one meeting and were not permitted to take detailed notes.
The complainant, a 44-year veteran of the industry, who has previously taken the department to court over a licensing dispute, also sought to raise his own licensing problem with officials. But it is understood officials informed the complainant both issues would have to be dealt with separately.
Subsequently, on October 4, the former skipper wrote to 12 EU fisheries ministers, the EU Commission and the Advocate General of the European Court of Justice alleging fishermen in Killybegs were showing a "blatant disregard for quotas".
"On a daily basis the tonnage of fish being caught far exceeds the allowable catch as laid down by the quota," the letter reads.
KFO chief executive Sean O'Donoghue last night confirmed the organisation had been contacted by the former skipper in July but said he stood 100% by the record of his members.
"We don't condone any activity that he is suggesting nor are we aware of anything like that happening.
"We have nothing to hide. He is making serious investigations and they need to be investigated," he said.
The EU also said last night it would investigate the allegations.
"It is Ireland's responsibility to properly implement the rules. We have taken action against Britain, Spain and Portugal for misreporting in the past and we will not hesitate to do the same in any other cases," said fisheries spokesman Gregor Kreuzhuber.