Ravikant Tupkar, state president of the farmer organisation Swabhimani Shetkari Sanghatana, resigned on Thursday.
He said he had sent his resignation letter to the Sanghatana's chief Raju Shetti.
Tupkar had met Maharashtra Chief Minister Devendra Fadnavis on Wednesday.
Asked about rumours that he was going to join the ruling BJP, Tupkar remained non-committal, saying he will take decision after consulting his followers.
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