Voting, which began at 7 am, will end at 5 pm.
The booths, where re-polling is taking place, include 63 in Murshidabad, 52 in Coochbehar, 28 in West Midnapore and 10 in Hooghly among others.
The State Election Commission had ordered the re-poll, following complaints of violence during the polls on Monday.
The poll panel has asked the state government and the police to make elaborate security arrangements so that polling can be held in a free and fair manner.
The counting of votes will be held on May 17.
The panchayat elections in West Bengal saw huge-scale clashes on Monday between the Bharatiya Janata Party (BJP) and the Trinamool Congress (TMC) workers, resulting in the death of at least 12 people.
The Congress, Communist Party of India (Marxist), Revolutionary Socialist Party (RSP) and other parties of the Left Front also staged a protest outside State Election Commission in Kolkata against the incidents of violence.
Taking note of the incident, the Ministry of Home Affairs also sought a report from the state government regarding incidents of violence during Panchayat Election in the state.
The voting took place for 621 zilla parishads, over six thousand panchayat samitis, and nearly 31 thousand gram panchayats. (ANI)