The strong performance by the opposition party comes days after it scored emphatic victories in the bypolls to two parliamentary and an assembly constituency.
The ruling BJP could win just one zila parishad seat, eight panchayat samiti seats and two municipal body seats for which byelections were held, they said.
Independent candidates won one zila parishad and one panchayat samiti seats.
An upbeat Rajasthan Congress chief Sachin Pilot said the result indicated a certain ouster of the BJP from the state.
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He said the Congresss voting percentage has increased in all the elections held in last four years whereas the BJP had to face debacles.
He claimed that in the Assembly elections due by the end of this year, a similar result would follow.
Chief Minister Vasundhara Raje has accepted the defeat in bypolls on parliamentary and assembly constituencies saying that it was a wake-up call and the result of panchayati raj institutions and local bodies declared today has indicated farewell of BJP from the state, he said.