Sayed Waqas, 24, was picked up along with four students at Vasantnagar area after the local cyber police found they have been circulating an anti-Modi MMS.
The four were released after being questioned, but Sayed was arrested under the IT Act, police said, but did not confirm when he was arrested.
Sayed, pursuing his MBA in a college at Bhatkal in Uttara Kannada district, is in the city for an internship. He was staying with the other students in a rented accommodation at Vasantnagar after police at Belgaum traced the mobile number to his residence.
The complaint was filed with Belgaum police by RTI activist Jayant Tinaikar, who said he had received the message on May 16, police said.
The incident comes a few days after a man from Mumbai was booked in Goa for posting a derogatory message against Mr Modi on Facebook.