President Mark Wales says escalating concerns about industrial wind turbines have prompted the group to make the recommendation.
Wales says farm families and rural residents must be assured that their interests are adequately protected in the development of wind farms.
The federation says it supports the intentions of the Green Energy Act, but notes wind power has been shown to be inefficient.
Energy Minister Chris Bentley says he's both surprised and disappointed at the federation's stance.
He says the group's position seems to have changed since December, when it issued a news release acknowledging its work with the government in developing the act.
"We've worked very closely with farmers, with the OFA, with rural Ontario in developing and strengthening the renewable energy approvals process," Bentley said.
"Working with the OFA, we brought in the new 550-metre setbacks," he said, referring to the required distance between homes and turbines.
Wales says the proliferation of wind turbines across rural Ontario has seriously polarized communities.
He says residents have been pitted against their neighbours over concerns with health impacts and quality-of-life issues relating to wind turbines.
"We are hearing very clearly from our members that the wind turbine situation is coming to a head — seriously dividing rural communities," Wales said Friday.
"The onus is on our provincial government to ensure the interests of rural Ontarians are protected," he added.
Opposition to large-scale wind farms cost the Liberal government some seats in rural Ontario in last fall's election. But Bentley points out that lots of farmers are making money from renewable energy projects.
"Thousands of farmers are already participating in renewable energy, including wind, and many thousands more are anxious to participate," he said.
Several lawsuits have been launched against wind farms attributing health issues such as sleep disturbances, headaches and memory problems to wind turbines.
Victor Fedeli, the Progressive Conservatives' energy critic, says his party introduced a private member's bill last fall that would have reinstated municipalities' powers to make decisions on such projects but it was voted down.
"The Green Energy Act stripped municipalities of all decision-making powers when it comes to wind and solar," Fedeli said.
Last February, the government halted development of off-shore wind farms.
Premier Dalton McGuinty has said the province will push ahead with land-based wind turbine projects.