Omar said on his twitter site, "I unequivocally condemn the attacks in Pulwama that left three political workers dead. By all means call for a boycott of the polls."
A village sarpanch, his son and another village head were killed in two separate attacks by guerrillas Monday in Amlar and Butgund villages of Tral town in Pulwama district.
The chief minister said the government did not force anyone to vote, why should the militants terrorize people not to vote.
"The decision to boycott should be based on conviction not fear. We don't terrorize people to vote so why instil fear to enforce boycott," he said.
The chief minister said the separatists knew it well that people would exercise their democratic right to vote if allowed to do so without fear.
"Using violence is an acceptance of the weakness of your argument because you know that in the absence of fear people will vote," he said.
Pulwama district is part of south Kashmir's Anantnag Lok Sabha seat that goes to the polls April 24.