Fadnavis, who said the government would announce the loan waiver before October 31, added that the modalities were being worked out.
About 1.07 crore farmers with less than five acres of land would be eligible for the waiver.
"I can say with conviction that this will be the biggest loan waiver in Maharashtra's history," Fadnavis told reporters after a meeting on urban development with Union Minister M Venkaiah Naidu here.
Prices shot up in various markets because of the short supply of vegetables and fruits. In Pune's Agricultural Produce Market Committee (APMC), the inflow of vegetables and fruits was half of that of regular days, which led to prices going up by three to five times, officials said.
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Fadnavis, however, said 300 of the state's 307 APMCs were operational yesterday, four had their weekly day off, while three were shut because of the ongoing agitation. Transactions were at 85 per cent of normal levels.
He also said workers of political parties, and not farmers, were indulging in violence and road blockades.
There was trouble in a few areas today. Farmers locked the offices of the talathi (revenue officer) in some villages in Kolhapur and Nashik districts.
The police took into custody 20 members of the Swabhimani Shetkari Sanghatna (SSS), who were holding a protest outside the collector's office in Sangli, and six SSS workers in Amaravati.
Meanwhile, market sources said the farmers' strike in Maharashtra had benefited traders from Surat, Belgaum, Indore and Delhi as the Vasai-Virar region was witnessing an influx of agricultural produce from outside the state.
The region has several vegetable markets with the produce usually coming in from Nashik, Junnar and Vashi. The stir had stopped the flow of vegetables from Maharashtra, they said.
The farmers' demand for loan waiver led government officials to do some arithmetic, with some estimating that it would cost the state Rs 30,000 crore.
Maharashtra's Finance Minister Sudhir Mungantiwar, however, refused to divulge the financial details, but said today the state was committed to helping the farmers.
Mungantiwar said the government was looking to cover the burden with the help of an additional Rs 10,000 crore mobilisation through non-tax revenues, 14 per cent growth in GSDP expected during the fiscal and also savings on expenses.
Chief minister Fadnavis gave a new twist to the stir, by stressing that road blockades were being carried out by political activists "hiding" behind farmers.
He ruled out consulting "those seeking to make political gains" and said he would talk only to "true" farmer leaders.
The farmers' protest, which has rocked various parts of the state since the beginning of the month, has also exposed fissures in the ruling coalition in the state.
The BJP-led government's allies Shiv Sena and the SSS are supporting the agitation.
SSS leader Raju Shetti said his party would soon decide if it would continue to be a part of the BJP-led government.
The Lok Sabha MP from Hatkanangle said he was "remorseful" to be a part of the Fadnavis government.
"What should be done about it (on being a part of the state government) will be decided in a forthcoming meeting," he said in Miraj, about 385 km from here.
The Sena pointed out the government was considering suspending internet services in Nashik, where the agitation has been particularly intense.
It added that the Sena would continue to support the strike till the end.
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