As much as Rs 22 crore would be waived as a result of the Centre's nod to the proposal, he told PTI.
The Centre had communicated its approval to the government a couple of days ago, he said.
A spokesman of the Department of Cooperation said loans were due from farmers to nearly 65 cooperative societies since 2007.
The waiver will benefit around 6,700 farmers in Puducherry and Karaikal regions.
The crop loan waiver was one of the many issues over which Puducherry Lt Governor Kiran Bedi and the Congress government had been at loggerheads.
She had then forwarded it to the Centre to get clarifications on whether the loans due to the nationalised banks could also be waived, he said.
He said the Centre's nod now would pave the way for the societies to consider sanction of fresh loans to farmers.
"This will also be a relief to the farmers, who were facing the impact of the vagaries of monsoon', he contended.
Agriculture Minister R Kamalakannan said the quantum of loans due from farmers to societies was only a 'pittance' compared to the amount waived in bigger states like Uttar Pradesh.
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