State Election Commission (SEC) sources said the TMC was also ahead in 2,317 gram panchayat seats for which counting is in progress.
The BJP has won 2,079 seats and is leading in 200 seats, while the CPI(M) captured 562 gram panchayat seats and is ahead in another 113, the SEC sources said.
The Congress won 315 seats and is leading in 61 seats, they said.
Independent candidates have won 707 gram panchayat seats and are leading in 120 seats.
According to the SEC, the TMC has so far won 95 panchayat samiti seats and is leading in another 65, while the other parties are yet to open their accounts.
In zilla parishads, the TMC has won 10 seats and is leading in 25 seats.
The BJP emerged as the main challenger to the TMC in gram panchayat in almost every districts except Murshidabad and Malda, the two Congress strongholds.
In Murshidabad, the TMC has bagged 466 seats, followed by the Congress with 83 seats.
In Purulia, the BJP is marginally ahead of the TMC in gram panchayats with 275 seats as against the 262 won by the ruling party till 2 pm, the SEC said adding that the Congress and the CPI(M) had bagged 60 and 44 seats respectively.
In South 24 Parganas, the TMC bagged 1,028 gram panchayat seats, followed by BJP with 177, CPI(M) with 72 and the Congress with 16.
In East Midnapore, the TMC won 1,075 gram panchayat seats, the BJP 74, the CPI(M) 55 and the Congress 5 seats.
The panchayat elections were held for 621 zilla parishad, 6,123 panchayat samiti and 31,802 gram panchayat seats in 20 districts of West Bengal on May 14.
The counting of votes began at 8 am today amid tight security.
Of the 48,650 seats in gram panchayats, 16,814 went uncontested. There was no contest for 3,059 of the 9,217 panchayat samiti seats.
In all, 203 of the 825 zilla parishad seats were uncontested, SEC sources said.