The farming organisation has come out swinging against Southland Fish & Game over what it calls "persistent, belligerent anti-farming rhetoric".
Federated Farmers Southland president Jason Herrick said the call to action was sparked by a court decision which would require Southland farmers to apply for a resource consent to keep farming lawfully.
Southland Fish & Game and Forest & Bird were pleased with the decision, saying it would help the province's heavily degraded rivers and waterways.
Mr Herrick said in a statement the decision was the last straw for his members.
"Southland Fish & Game were one of the main groups pushing for that decision, which is an absolute kick in the guts for farmers down here."
Farmers had always allowed anglers to walk across their land but that goodwill had now been eroded.
"We’re fed up with Southland Fish & Game’s persistent, belligerent anti-farming rhetoric and their opposition to everything we do.
"We’ve tried our best to maintain our relationship with them, but they’ve washed that relationship away down the Mataura River.
"We’re now calling for local farmers to join us in boycotting fishing licences, and to remove fishing access by taking down access signs."
Federated Farmers suggested its members replace access signs with an orange ribbon.
The boycott call applied to Southland only, he said.
Southland Fish & Game manager Zane Moss said in a statement the organisation worked closely with farmers and understood their challenges.
He noted Southland Fish & Game was involved in the recent Environment Court where it gave evidence alongside parties including Federated Farmers.
"Based on the evidence, the court concluded our rivers were significantly degraded by diffuse discharges, and that the rules in the proposed Southland Water and Land Plan weren't sufficiently robust to ensure that it didn't continue.
"Environment Southland should put effective rules in place around the riskiest practices so all farmers are not required to seek consents."
