The Irish Farmers’ Association national executive has unanimously voted to recommend a Yes vote in the Lisbon Treaty referendum to its members.
The move comes after the Taoiseach issued a statement this morning saying Ireland would reserve the right to veto a proposed World Trade Organisation (WTO) agreement if necessary.
Mr Cowen, who earlier met with the IFA, said that he had reiterated his view that the current proposals for a WTO deal were unacceptable.
Crucially for the IFA, which had been looking for a harder stance from him, Cowen used the word veto three times in his statement.
"The Taoiseach assured the IFA that he was prepared to use the veto if a deal that is unacceptable to Ireland is put to a vote," the Taoiseach's office said in a statement.
The statement said unanimity was required for EU approval of the outcome of the current WTO negotiations and therefore “Ireland can veto EU agreement to an unacceptable deal”.
“The Lisbon Treaty would not change these arrangements or the existence of this veto,” the statement added.
The IFA had declined to recommend a Yes vote in the absence of a Government commitment to veto the WTO deal that it claims would be damaging to Irish agriculture.
A planned meeting of the IFA Executive Council was delayed this morning while its president, Mr Pádraig Walshe, met Government representatives.
However, after reconvening the Executive Council this afternoon, Mr Walshe said that "the way is now clear for farm families to vote Yes in the Lisbon Treaty Referendum."
He said he was satisfied that IFA had secured the clarity farmers needed on the use of the veto in the WTO negotiations to protect Ireland's vital national interests in Agriculture and particularly the Irish livestock and beef industry.
"The farming community and rural Ireland can be assured by the Taoiseach's statement on the veto today that the WTO deal on the table in Geneva is not acceptable to Ireland and that any agreement in the future must not undermine our agriculture interests", he said.
Speaking on the campaign trail in Cork, Mr Cowen insisted there was no change in Government policy despite today's decision to invoke the veto if required.
"The statements of Micheal Martin, Brendan Smith and my own statement are consistent.
"In relation to the Lisbon Treaty referendum, if I can be of assistance to any organisation in clarifying issues, I have always been available to do so."
Former Green Party MEP and chairperson of the anti-Lisbon Treaty People's Movement Patricia McKenna was sceptical of the assurances given by the Taoiseach.
"It would be nice but foolish to believe that the Irish government would use its veto to protect Irish family farming at the expence of a WTO agreement for the entire EU."
"Farmers know this, their leadership knows this, the government’s “promise” extracted under pressure, was given in a futile attempt to save the Lisbon treaty, this promise is as empty as those given to growers of the now abandoned sugar beat industry," she said.
Fianna Fáil's four MEPs Brian Crowley, Liam Aylward, Sean O Neachtain and Eoin Ryan welcomed the IFA decision and said a Yes Vote would allow Ireland to continue to negotiate issues of importance in Europe "from a position of strength and not from a position of weakness."
Fine Gael Agriculture Spokesman, Michael Creed TD, also welcomed the IFA’s announcement saying: “The Lisbon Treaty will benefit farmers and I look forward to a push for a ‘Yes’ vote from the farming organisations over the next 10 days.
On Sunday, the country's second largest farmers organisation, the Irish Creamery Milk Suppliers' Association (ICMSA) decided to recommend a Yes vote in the Lisbon referendum to its members.
This followed a meeting with Taoiseach Brian Cowen at which he assured them that the Government would not accept a World Trade Organisation (WTO) deal that was unbalanced and undermined farmers' interests.