"This draft notification can have a huge negative impact on India's cotton sector and will have deep rooted ramifications for all other knowledge and innovation driven sectors," it said in a statement.
The draft notification has serious implications for research and innovation in the country, Assocham said.
"By trying to determine the price of technology, overriding existing commercial contracts of technology providers and introducing essentially compulsory licensing provisions, it may send a negative message," it added.
This could also have ramifications across R&D and technology intensive sectors such as pharmaceuticals, telecom, it said adding it would also have the potential to dampen investor interest in government's 'Make in India' initiative.
"The government instead of dictating the licence terms and artificial price controls, should focus on creating an environment that encourages research and recognises the benefit that these technologies bring to farmers," the chamber said.
Amid opposition from crop biotech industry, the government has last week withdrew a notification capping royalty for new genetically modified (GM) traits and would now seek comments from stakeholders before taking a final call.