That apart, the royalty fee or trait value payable by domestic seed firms to technology developer Monsanto Mahyco Biotech (India) Ltd (MMBL) has been slashed to Rs 39 per packet from Rs 49.
The new prices will come into effect from the 2018 kharif season starting June. A packet of Bt cotton seeds is of 450 gram.
The move will benefit 8 million cotton growers, but will reduce the margin of domestic seed companies and also MMBL.
For the BG-I version, the maximum sale price has been kept unchanged at Rs 635 per packet with no trait value, the notification added.
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A senior ministry official said the reduction in price will provide some relief to cotton farmers who have been affected by repeated pest attacks and crop losses.
The government started controlling prices of cotton seeds including the GM versions, by fixing a uniform maximum sale price from March 2016.
Cotton production is estimated at 33.92 million bales (of 170 kg each) in 2018-19 crop year as against 32.58 million bales last year.