The Feb. 13 ruling by Supreme Court Justice Nunes Marques relates to a GMO technology commercially known as Intacta RR2 Pro, created by Monsanto, which was later acquired by Germany's Bayer.

Bayer said in a statement it will determine its next steps while noting it would comply with the ruling.

The ruling is the latest chapter of a protracted battle opposing the crop science firm and Brazilian farmers, who have launched multiple legal challenges against the firm.

In 2017, Mato Grosso farmers sued Monsanto over that same genetically modified seed, seeking to cancel its patent protections by claiming it did not bring any technological innovation.

Two years later soy producer associations in 10 Brazilian states joined that lawsuit.

Aprosoja-MT said that according to the ruling, Bayer will now have to deposit 1.3 billion reais ($252 million) in an escrow account to return royalties paid by farmers going back to 2018.

Bayer said it is analyzing the Marques ruling, which refers specifically to a lawsuit brought by farmers claiming the company was charging royalties on a patent that had expired.

"It is worth mentioning that the Intacta RR2 Pro technology is protected by intellectual property rights of a wide and diverse nature," Bayer said. "We trust that these rights give us legal support so that the use of our protected technology is respected in the country."

A lawyer for Aprosoja-MT said Bayer can appeal Marques' ruling at the plenary of the Supreme Court.

Brazilian cotton producers have also sued Bayer over Bollgard II RR Flex genetically modified cotton seed. ($1 = 5.1673 reais)

(Reporting by Ana Mano; Editing by Sandra Maler)

By Ana Mano