The U.S. agricultural products company said it is seeking extension of the patent on its Roundup Ready soybean seed, used by millions of Brazilian farmers, to counter the claims.
The dispute assumed epic proportions last year when millions of Brazilian farmers sued Monsanto over what they claimed were overpayments of royalties on genetically modified soybean seeds.
The court ruled in favor of the farmers, saying Monsanto owes them at least $2 billion paid since 2004.
Brazil is the largest producer of genetically modified agricultural produce after the Unites States and a major customer for Monsanto.
The company is seeking to resolve the dispute and secure its proprietary rights before it starts to sell another modified seed.
Monsanto said it will "move forward with the next phase of the appeals process to secure its intellectual property rights and ensure its business isn't disrupted in the country."
Monsanto previously obtained patent protection in Brazil for its first-generation Roundup Ready soybean products. It sought to correct the term of its patent rights in Brazil to conform to a 2014 patent term granted in the United States.
Monsanto seeks to have the ruling by a single superior court judge overturned by a full panel of supreme court judges.
"We plan to file an immediate appeal with the Superior Court of Justice and look forward ultimately to presenting our case to the Supreme Court of Brazil at a later date," Todd Rands, Monsanto's legal director for Latin America, said in a statement.
Monsanto said it remains "committed to ongoing dialogue with farmers and their representative groups in order to pave the way for innovation in agriculture, as this is one of the critical paths toward delivering value to Brazil's farmers and its economy and meeting the demands of our growing planet."
The company faced further opposition from farmers after it proposed a compromise rejected by farmers' representatives.
Carlos Favaro, president of the Mato Grosso association of soya-bean and corn producers, earlier outlined reasons for farmers' opposition, Nature magazine reported.
He agreed that intellectual property is important and that ceasing royalty payments could affect research.
But he said the current system is untenable.
"The way of collecting royalties is unfair, (Monsanto) charges us in double: when we buy the seeds and then when we sell the soy," Nature reported on its website.
Agriculture industry researchers said they feared the dispute could affect funding especially as some Brazilian biotechnology research bodies have lucrative partnerships with Monsanto.
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