IFA members in Donegal have declared no confidence in the association's National Executive, and have called on the board to resign.
However, a motion that no confidence be declared in the County Executive was rejected.
Last night's emergency meeting in Letterkenny was called to discuss the fall out from the pay and pensions scandal which has dominated the national headlines for the past week.
Around 300 farmers attended the emergency meeting, which was addressed by IFA officials from Donegal and Ulster.
The meeting passed a motion of no confidence in the National Executive of the IFA, and called on it to resign.
A vote of no confidence in the county executive was proposed, but when a counter proposal expressing support for local officials was tabled, it received the support of a substantial majority of those in the room.
The meeting also referenced the current review into IFA payments being conducted being conducted by former chief economist Con Lucey, saying the legal and accountancy advice should be subject to scrutiny.
The meeting also said that an independent external auditor be part of that review, and that details be given of the salaries of all past presidents since payments were first made.