Scientists advising the Government's National Salmon Commission did not seek an immediate drift net ban from the end of this season to try to conserve wild salmon stocks.
A key scientific report on the issue was also not debated by commission members before last week's controversial vote in favour of a drift net ban.
Instead, an interpretation of scientific advice by managers of the State's regional fishery boards - who concluded that a drift net ban was necessary - was put to a vote and carried by a majority of one, with two abstentions.
The recommendation is now before Minister for the Marine Noel Dempsey, without any agreement on a phased voluntary buyout or a compensation package for licence holders.
This sparked a protest by licence holders from Donegal to Kerry in Galway last week.
Marine survival of salmon is at its lowest since the current national assessment began in 1980, according to the salmon commission's scientific committee. In a report in late January on the 2006 season, the committee said that overall exploitation in most districts should immediately decrease.
The report said mixed stock fisheries, where salmon from different river systems are caught at sea, presented particular threats to the status of individual stocks.
"It is recognised that it may not, for practical reasons, be possible to move to single stock fisheries immediately," the report stated. Asked at the January meeting if this meant a drift net ban, one of the scientific committee members stated it did not.
A previous report by committee member Niall Ó Maoileidigh, of the Marine Institute, and Ted Potter, of the British Centre for Environment, Fisheries and Aquaculture Science, noted that Ireland was not the only EU member state continuing to allow commercial fishing for salmon - it still continues on a small scale in England and Sweden - and warned that a ban on mixed stock fishing, rather than a phased voluntary buyout, might increase illegal fishing.
The salmon committee, chaired by Joey Murrin, has been endeavouring to broker a voluntary buyout of the drift net fishery, as recommended in a recent joint Oireachtas committee report. A similar scheme is being implemented in northeast England.
Instead of voting on the scientific committee's advice, the salmon commission voted last week on a report by managers of the State's eight fisheries boards which concluded that the advice meant a drift net ban was necessary.
Bord Iascaigh Mhara's representative on the commission, Michael Keatinge, abstained from the vote, and told The Irish Times that as a public servant he did not consider it appropriate to vote on an issue that has "significant implications for two groups of stakeholders".
Several other commission members told The Irish Times that they were shocked at what occurred at the meeting.