Irish Farmers' Association (IFA), which belatedly pledged support for the Lisbon Treaty, tonight warned of a looming blame game.
The 85,000-strong organisation backed the Yes campaign 10 days ago, giving the Government a huge boost but officials said local issues had ultimately taken over.
The IFA said many people feared the treaty would impact on Ireland's Defence Forces and their peacekeeping role and also religious affairs.
However, the group's chief executive Padraig Walshe urged all sides to work together to repair the damage done by the resounding No vote.
"Political parties and their leaders who had supported the referendum should not engage in a blame game as this would be fruitless," he said.
The IFA only moved to support Lisbon after the Government assured members it would veto any world trade deal that undermined Ireland's agricultural interests.
It came as a huge relief for Taoiseach Brian Cowen, and with a potential 85,000 votes or more from farmers and their families it appeared to secure the necessary numbers to pass the referendum.
An IFA spokesman rejected suggestions they did not get the vote out or that farmers did not follow the advice from leaders.
"Our tracking tells us not only did our people turn out but they turned out and voted Yes in strong numbers. We are quite confident about that," the spokesman said.
"What we were getting back in the last few days was that people voted No for a lot of different reasons, military, religious and local domestic issues.
"You had a myriad of issues which contributed to a No vote but we are happy that our membership took our advice and got our vote out."
The IFA claimed local issues including protests by fishermen in Co Waterford over high operating costs and quotas and hospital issues in the North-West were to blame for the No vote.