It said the decision to control cotton seed prices was taken without consulting the body or its member companies.
"ABLE-AG also questions the decision making process that involved no prior information, discussion, or consultation by the Ministry with the association or any of its constituent organisations or technology developer and provider and any other Stakeholder in general," the industry body said in a statement.
The Association of Biotech Led Enterprises - Agriculture focused Group (ABLE- AG) has also written a letter in this regard to the Prime Minister's Office.
"We believe such a step hampers confidence in making investments in innovative research & development and is contrary to the Government's 'Make in India' campaign and impacts ease of doing business," ABLE-AG Director General Ram Kaundinya said.
In a notification issued earlier this month, the Union Agriculture Ministry has decided to control prices of cotton seeds including the genetically modified versions by fixing a uniform maximum sale price from March 2016.
The notification was issued at a time when there is a tussle between the Mahyco Monsanto Biotech (India) Ltd (MMBL) and seed companies over payment of royalty for using Bollgard technology in hybrid cotton seeds.
Bt cotton is the only GM crop allowed for commercial cultivation in the country. Over the last decade, Bt cotton technology has been adopted on over 95 per cent of the country's cotton growing area, making India the second largest producer and exporter of cotton.