Collector Nila Mohanan relied on a report submitted by the police which said that with Panaji Assembly by-election coming up, Muthalik's visit might lead to a law and order situation and communal tension.
Muthalik last week had sought permission to visit the state for ten days. At present he has been prohibited from entering the state.
He had announced last year that he would be establishing a unit of his outfit in Goa, and it would make people aware about dangers of "pub culture" in the state.
Takbhate had also said that denial of permission would be a violation of his client's fundamental rights.
Ram Sene, a Hindu right-wing organisation, became infamous after an attack on a Mangalore pub in 2009.