At main market at Pandharkawda in Yavatmal district, traders and farmers decided to suspend transactions till next week when old notes get replaced with new denominations of Rs 2,000 and Rs 500.
Cotton and soyabean are main cash crops in Vidarbha region in east Maharashtra.
The arrivals in cotton markets started only recently due to extended rainy season this year.
When cotton markets reopened today, farmers refused to accept notes of higher denominations as traders did not have enough Rs 100 notes to make payment for cotton which is fetching Rs 4,800 per quintal.
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He, however, clarified that there was no panic as such in the market.
"Farmers and traders are ready to wait till the currency issue is resolved," said N P Hirani, Chairman of Maharashtra State Cotten Growers Co-operative Marketing Federation.
He said life in countryside is not much affected following the government's move to scrap Rs 500 and Rs 1,000 notes.
"Small businesses and village stores are accepting Rs 500 and Rs 1,000 for now towards the purchases made by farmers as they know they can get the old notes exchanged when banks reopen on November 10," Hirani said.