Reports say Manjunath, a native of Bantwal, was roughed up by the youths so saying "this is Hindu Rashtra and Muslims should not come here".
According to the police, a verbal altercation over tea led to the assault. Police said action would be taken against those who assaulted the youth based on video evidence.
Manjunath filed a complaint at the Pandeshwar police station and a case has been registered, police told news agency PTI.
The video of the assault went viral on social media post which the city police commissioner P S Harsha asked people not to sensationalise the issue, saying it was an isolated incident.
Action will be taken against the attackers, he assured.
Mangaluru is considered to be a communally sensitive region in the southern state of Karnataka.