The Agriculture Ministry on December 7 had issued Cotton Seeds Price (Control) Order to fix a uniform maximum retail price (MRP) on all cotton seeds, including the genetically modified versions, from March.
It also decided to fix and regulate the seed value and licensee fee, including royalty or trait value.
In three different letters to the National Seeds Association of India (NSAI), the companies said the body's support for price regulation will have wide ramifications.
The companies also said the NSAI actively sought nationwide regulation of cotton seed prices.
"We also understand that the NSAI has sought to defend the Cotton Seed Price Control Order in the court despite having in the past challenged other price regulations before various courts.
"We urge NSAI to refrain from pursuing such action presently and consult and obtain concurrence of all its member companies," it added.
The Centre's order comes at a time when there is a tussle between the Mahyco-Monsanto Biotech (India) Pvt Ltd (MMBL) and seed companies over payment of royalty for using Bollgard technology in hybrid cotton seeds.
MMBL on December 19 had filed a writ petition in the Delhi High Court challenging certain provisions of the order that seeks to regulate licensing of cotton seed technology.
Bt cotton is the only GM crop allowed for commercial cultivation in the country. Over the last decade, Bt cotton technology has been adopted over 95 per cent of the cotton growing area, making India its second largest producer.
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