Voters in 12 booths under Shruti and Khargram blocks boycotted poll to protest against some local grievances including bad roads and no electricity.
The sub-divisional officer of Murshidabad district and other high officials have gone to the booths to convince voters to exercise their franchise.
A few EVMs malfunctioned in some booths in the morning, delaying the start of polling but were repaired soon to enable its resumption.
The district magistrate, Rajiv Kumar, said the long border with Bangladesh in the district had been sealed. Ten companies of central forces are manning the sensitive areas.
There is an electorate of 12,40,000 in the Lok Sabha seat from where Pranab Mukherjee had been elected regularly prior to his elevation to the highest office in the nation.
The by-poll was necessitated by the resignation of Pranab Mukjerjee.
Trinamool Congress has not put up any candidate against Abhijit Mukherjee as a political gesture despite severance of ties with the Congress.
Mukherjee is pitted against Muzaffar Hussain (CPI-M) and Sudhangshu Biswas (BJP) in a multi-corner contest.
Lesser voting percentage in Jangipur LS by-election
Sixty per cent polling was recorded in the by-election to Jangipur Lok Sabha constituency in West Bengal today as against 84.71 per cent polling registered for the same seat in the 2009 election.
However, the polling figures are set to go up as many voters were still standing in the queue in many booths even after voting was over at 5 pm, West Bengal chief electoral officer Sunil Gupta said.
The by-election was incident-free, he said.
However, voters boycotted exercising their franchise in 26 booths on development issues and Murshidabad district magistrate held series of meetings with those who gave call to boycott voting.
The by-poll was politically significant with President Pranab Mukherjee's son Abhijit Mukherjee contesting as one of the 11 candidates.
In the last assembly election in 2011, Jangipur recorded 85.97 per cent votes, he said.
The constituency has a total electorate of over 12.41 lakh.
Out of the 1,530 polling stations, 208 were declared sensitive and 379 critical.