Worst hit are the farmers in Karimnagar and Warangal districts, where cotton is predominantly cultivated.
They complain of tedious waits at the counters and the lottery system to allocate the seeds.
Farmers from Husnabad and Warangal also alleged that resourceful farmers from Seemandhra are paying a premium to acquire seeds meant for Telangana farmers.
Underplaying the allegations, Andhra Pradesh Seedsmen Association Secretary Venkat Reddy claimed that the association has succeeded in meeting 86 per cent of the demand while efforts are underway to meet rest of the demand.
He clarified that one of the 42 seed manufacturers has failed to meet the production target due to inclement weather conditions, resulting in the alleged shortage.
Farmers have been insisting on particular brands of seeds, leading to the present irregularity, Reddy said.
“The problem will be solved if the farmers accept alternate variety of seeds, which, in all probabilities, will give desired yield.
All hybrids are approved by the Genetic Engineering Approval Committee (GEAC), Government of India,” he said.