BRASILIA, Brazil — Brazilian farmer groups oppose a contract that Monsanto Co., the world’s biggest seed company, is offering farmers to end a dispute over royalty payments on its genetically modified soybean seeds.

Monsanto is trying to resolve uncertainty over its ability to collect fees on its new Intacta soybeans, which the St. Louis-based company is scheduled to start selling in Brazil during the next growing season.

The contract would waive royalties on Roundup Ready soy, an older technology, this year and next. In return, farmers would forgo claims in a patent dispute and pay royalties on seeds not yet on the market. The future payments are opposed by the Brazilian National Agriculture Federation, a group of farming associations also known as CNA.

Associations unite against Monsanto

“We reject the individual contracts offered by Monsanto,” Katia Abreu, the head of CNA, said Wednesday in an emailed statement…