"Only one company had raised the issue. From the time the law was made, for the past two years, no one had raised any objections that it is not WTO compliant," Nath said on the sidelines of signing an agreement with Switzerland on intellectual property rights.
Nath said time had proved that the Indian law that denied patents for minor improvements to known drugs did not lead to any increase in prices.
"When this law was made, I had told in the Parliament that prices will not rise. It has been two years, and time is the biggest witness that the prices have not risen because of the law," he said.
The court rejected the challenge, saying it had no jurisdiction on whether Indian patent laws complied with intellectual property rules set by the WTO, as Novartis had questioned.
Novartis is expected to make a statement soon on the court order.
Novartis had filed a similar case against the South African Government in 2001, which tried to roll out HIV anti-retro viral drugs in its own country by granting licenses.
The Swiss company has said the Indian patent system stifles innovation.
Critics of Novartis say changes to the law would affect the supply of affordable anti-AIDS drugs from India, one of the biggest makers of generic drugs.
Novartis had moved the Madras High Court against a law that blocks the patenting of minor improvements in known molecules.
The Swiss pharmaceutical firm argued tightening of intellectual property laws would increase investment for developing more drugs.