Farmers have told National Parks and Wildlife Service rangers and BirdWatch Ireland members to stay off their lands until a compensation agreement over habitats in Special Areas of Conservation is honoured.
The agreement was negotiated in 2003.
At a meeting in Co Offaly, the IFA said it will post notices on farm gates all over the country advising the NPWS to keep out until a new government meets the terms of the original deal.
IFA SAC Project Team Chairman Tom Turley said the NPWS Farm Plan Scheme will have to be available to all farmers who have a designation imposed on their land and the new agreement on SACs has to be implemented before the end of 2016.
In relation to flooding, he said the refusal of NPWS to allow remedial works to take place on rivers has contributed to severe flooding in certain areas.
He said: "Dredging of rivers will have to take place to alleviate the problems associated with flooding. NPWS cannot be allowed to stand in the way of this".
Mr Turley also said that farmers who want to plant trees in areas designated for the hen harrier must be allowed to maximise the potential of their land.
He added that existing restrictions that have impeded improvement and other development works in designated areas must be relaxed as they are adding to economic decline in rural areas.
The NPWS is a section of the Department of Arts, Heritage and the Gaeltacht.
In a statement, the department said: "The DAHG, together with the Department of Agriculture, works closely with the IFA on a range of issues, including the management of land in designated areas in order to protect our heritage.
"It is inaccurate to suggest that the NPWS has obstructed flood alleviation works.
"The department is strongly committed to working with the IFA and other farming organisations to the benefit of those living and working in rural Ireland."
BirdWatch Ireland have said they are "extremely surprised" at the campaign.
The organisation said they enjoy "a very good working relationship with farmers and landowners around the country", adding that they have advocated for financial support for farmers who are in a position to hep wildlife.