The decision, which upholds earlier rulings, will be seen as a blow for global drugmakers' efforts to hold on to exclusivity on high-price medicines in India.
Indian generics group Natco Pharma said the highest court had dismissed Bayer's challenge to a compulsory licence allowing it to sell a copycat version of the medicine, which is used to treat kidney and liver cancer.
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But Bayer has been fighting this compulsory licence, arguing that it weakens the international patent system and endangers pharmaceutical research.
The German group said it was disappointed by the Supreme Court decision and its legal experts were evaluating the verdict. "We are analysing the order and will determine any future course of action afterwards," a spokesman said.
Natco was first given permission by the Indian patents office in 2012 to sell generic Nexavar at 8,800 rupees ($141) for a month's dose, a fraction of Bayer's price of 280,000 rupees. Bayer challenged this decision in the long-running case.
Western pharmaceutical groups have a lengthy history of patent problems in India, which has a thriving generic drugs industry and a large population for whom patented drugs are unaffordable.
In a much higher profile case last year, Swiss drugmaker Novartis suffered another defeat in the Indian Supreme Court when its attempt to win patent protection for its cancer drug Glivec was dismissed.
Indian courts have in recent years also revoked patents granted to other international drugmakers, including Pfizer , Roche and Merck.
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