The Marine Institute has been asked to hand over confidential research information to the Garda as part of its investigation into alleged fraud within the fishing industry.
The request is understood to have come in recent weeks from the Department of Communications, Marine and Natural Resources, the institute's principal source of funds, even though gardaí confirmed last month that a file on their investigation had already gone to the Director of Public Prosecutions.
Both the department and the institute have told The Irish Times they cannot comment. However, it is understood that institute board members were told this week that information has been given to the department, but not to the gardaí.
Scientists at the institute are believed to be seriously concerned about the impact of any such move on their relationship with the fishing industry.
Marine scientists have enjoyed a healthy relationship with individual fishing skippers as part of continuing EU and State-funded marine research programmes. Regular sampling, including monitoring discards of fish, is used to inform EU fisheries ministers in their annual deliberations on total allowable catches and quotas, and conservation programmes for individual stocks.
The Garda investigation into alleged irregularities within the industry and alleged collusion with department officials was initiated just over a year ago by Marine Minister Noel Dempsey, following claims made to the European Commission by Donegal fisherman Pat Cannon.
Mr Cannon, who had apparently been refused a licence for a fishing vessel, claimed that there was widespread fraud, including overfishing of quotas and misreporting of catches and that department officials were involved.
Several raids on homes and on fish catching and processing businesses in ports from Killybegs, Co Donegal, were carried out by investigating gardaí. Vessels, businesses and factories were also checked in several west and southwest ports, including Rossaveal, Co Galway, and Castletownbere, Co Cork.
In October gardaí confirmed that a file had been sent to the DPP. Much of the focus of this investigation had been on pelagic (mackerel/herring) landings, but the information sought from the institute relates to whitefish landings.
Parallel to the Garda investigation has been the introduction of a new piece of fishery control legislation.
There has also been a severe crackdown on Irish fishing vessels by the Naval Service and department officials.
"Ironically, this is at a time when the European Commission has taken a new approach to fisheries management involving regional advisory councils comprising elected stakeholders," Lorcan O'Cinneide, chief executive of the Irish Fish Producers' Organisation, said.