Is Prime Minister Narendra Modi expected to respond each time a "dog dies in Karnataka", Muthalik asked in a reference to the murder of Gauri Lankesh.
"Everyone is saying that Hindu groups conspired to kill Gauri Lankesh, but two murders in Maharashtra and two in Karnataka took place during Congress' rule," he was quoted by PTI as saying said.
He referred to the killings of rationalist Narendra Dabholkar, Left leader Govind Pansare, Kannada writer M M Kalburagi and Lankesh.
"No one questioned the Congress government's failure... instead these Left-leaning intellectuals ask Prime Minister Narendra Modi to speak on Gauri Lankesh's death," he said.
"Do you expect Modi to respond every time a dog dies in Karnataka?" he asked.
Offering a clarification, Muthalik later said he only pointed out that prime minister cannot comment on each and every death in the state.
Slamming Muthalik for his statement, Congress leader Manish Tewari termed his remark as "disgusting and "nauseating".
"Disgusting, nauseating, revolting... vigilante group Sri Ram Sene's Head Pramod Muthalik compares assassinated journalist Gauri Lankesh to a dog."
"Mr Prime Minister @narendramodi you did not condemn Gauri Lankesh's murder are you now going to condone this too," Tiwari said on Twitter.
The Sri Ram Sene came under the police scanner after the Special Investigation Team probing the Gauri Lankesh murder case recently summoned Rakesh Math, the Vijayapura district president of the fringe right-wing outfit, for questioning.
Lankesh, 55, the Editor of "Lankesh Patrike", was shot dead outside her residence in the city's suburb by unidentified assailants on September 5 last year. She was a left-leaning journalist and a strong Hindutva critic.
According to the police, of the total seven bullets fired by the unidentified men, three had hit Lankesh -- two in the chest and one in the forehead.
(With inputs from agencies)