Prajapati said he has sent the resignation letter to party President Sonia Gandhi.
He is also president of the Akhil Gujarat Prajapati Sangh which represents over 80 lakh-strong Kumbhar community in the state, where elections are to be held for civic bodies and tehsil panchayats in October and November.
He told PTI that he was quitting Congress after serving it for 40 years because of "internal politics" and he did not rule out the possibility of joining the ruling BJP.
"The party has been showing little concern for poor people and their plight," he said.
His younger son, Vishnu Prajapati, is a member of BJP while the elder son Rajesh Prajapati is vice president of the city unit of Congress.