The Delhi High Court on April concurred with Indian seed company Nuziveedu Seeds Ltd (NSL), which argued that the Patent Act does not allow Monsanto any patent cover for its genetically modified cotton seeds.
Monsanto has appealed to the Supreme Court, said a Monsanto India spokesman.
"In the Supreme Court, we'll maintain our stand that agricultural products, including seeds, cannot be patented in India," said Narne Murali Krishna, a company secretary for NSL. "The judgement of the Delhi High Court has already vindicated our stand."
New Delhi approved Monsanto's GM cotton seed trait, the only lab-altered crop allowed in India, in 2003 and an upgraded variety in 2006, helping transform the country into the world's top producer and second-largest exporter of the fibre.
Monsanto's GM cotton seed technology went on to dominate 90 percent of India's cotton acreage.
But for the past few years Monsanto has been at loggerheads with NSL, drawing in the Indian and US governments, Reuters revealed last year.
The fate of the biotechnology industry rests on the decision of the Supreme Court, said Ram Kaundinya of the Federation of Seed Industries of India, an industry body formed by the local units of foreign companies such as Monsanto, Bayer, Dupont Pioneer and Syngenta.
After last month's court ruling, nearly 107 patents could be deemed void, said Mr Kaundinya.
Seed makers are now scaling down and shelving their research projects, said Paresh Verma, chief of research at Shriram BioSeed Genetics India Ltd.
"It's a fluid situation and we've decided to reduce our research expenditure," said M Ramasami, chairman and managing director, Rasi Seeds.
Without the protection offered by the Patents Act, it is not clear how technology providers would be able to monetise their investments, said S Nagarajan, managing director and chief executive of Metahelix Life Sciences Ltd.