Macra na Feirme, the youth farm organisation, has decided to lift its boycott of Teagasc, the agriculture and food advisory body, which it imposed as part of the row over the nitrates directive.
Macra, the Irish Farmers' Association and ICOS, the umbrella group for the co-operative movement, also decided not to co-operate with Teagasc over the same issue.
This led to the cancellation of two of the most important farming events of the year, the Teagasc national tillage conference and its national potato conference.
However, Macra decided to end its boycott following the last meeting of the Teagasc board, at which revised advice on the application of fertilisers was put forward.
Macra national president Colm Markey said that, while he was not happy with the document, the matter had now been concluded at Teagasc level.
He said the boycott had been effective in putting the issues firmly on the Teagasc agenda and he acknowledged that there were recommendations in the new document that would relieve some of the pressure on farmers.
"It is regrettable that farmers had to take such an action against an organisation that had provided an effective service to farmers in the past, but it was absolutely necessary in the circumstances," he said.
"Farmer confidence in Teagasc is at an all-time low, and major changes will be required if the credibility of Teagasc is to be restored. However, I believe that at this point the responsible course of action is to lift the boycott," he said.
The national officers of the Irish Farmers' Association will meet on Thursday next and are expected to follow the line taken by Macra as the issue has been placed on the agenda of the scheduled meeting.
However, it is not thought the IFA will address the other issue which arose from the nitrates controversy, its withdrawal from the national partnership talks.