Agriculture Minister Sharad Pawar said during Question Hour that cotton production has risen from 164 lakh bales in 2004-05 to 340 lakh bales in 2011-12.
"This is clear cut indication that there is higher production (after use of Bt cotton)," he said.
Pawar said farmers in Dhule district of Maharashtra and Khargone district of Madhya Pradesh have complained of yield loss after using hybrid cotton seeds produced and marketed by Bayer Bio-Science Pvt Ltd.
The loss was suffered as both Dhule and Khargone received higher than normal rainfall, he said adding compensation has been awarded to farmers for the losses but Bayer Bio-Science has gone in for appeal.
The government, he said, does not prescribe what seed farmers use for growing crops. "Farmers decide which seed they have to buy," he said.
Nine states using Bt seeds, should make provisions in law that if "something goes wrong... if farmers suffer, there has to be provision where the company pays compensation," he said.