Parrikar said this in a written reply tabled Wednesday in response to a question by ruling Bharatiya Janata Party legislator Vishnu Wagh.
The chief minister also said that "no concrete evidence was found" to prove that Muthalik was attempting to create a communal divide in the state.
The issue of the Sene, known for ransacking a pub in Mangalore and attacking young men and women there, starting a branch in Goa has been heavily debated by politicians as well as civil society here.
Muthalik had called for a crackdown on what he called "pub culture" in Goa, which is known as the night-life capital in the country.
Muthalik had also said that he would distribute swords and Bhagwad Gitas to Hindus, exhorting them to use the weapon if needed.