Sinha, who is the sitting Lok Sabha MP from Patna Saheb, was shown black flags at Kargil Chowk while he was going to file his nominations for the Lok Sabha elections.
The youths who waved black flags at the BJP leader claimed themselves to members of NGO "Lokhit Vikas Manch"
The actor-politician was shown black flags by some protesters, which led to fierce clashes. Several persons were reportedly injured in the skirmish.
City Superintendent of Police Jaykant said that it was "a skirmish".
Though Sinha did not comment on the incident, which occurred for the second consecutive day, BJP MLAs, Nitin Navin and Prem Ranjan Patel, who accompanied him described it as the "handiwork" of political rivals.
"Most of the protestors were young and when asked the reason for showing black flags did not comment," Navin said.
Patel alleged that the protesters appeared to be drunk.
Earlier on Thursday, Sinha had to face similar protests from some BJP youth wing workers when he was on his way to the party office from Patna Airport.
A complaint was registered with the Kotwali Police Station for Thursday’s assault, Kotwali SHO, Alok Kumar said.
The complainants had named Sinha and his supporters for the assault, Kumar said.
Sinha popularly known as 'Bihari Babu', incidentally, had been opposed by a section of leaders in BJP. There were reports that senior BJP leader Ravishankar Prasad wished to contest from Patna Saheb. Due to resistance, the candidature of Sinha, who had served as cabinet minister in the Atal Bihari Vajpayee government, was earlier put on hold and his ticket was approved only in the second lot for Bihar.
Sinha would face Bhojpuri actor Kunal Singh of Congress, former Bihar minister and AAP leader Parveen Amanullah and JD (U)'s Gopal Prasad Sinha on April 17.
Meanwhile, Sinha thanked the BJP high command for honouring his wish to contest the polls from Patna Saheb.
Expressing his gratitude to the party, the BJP leader said that from now onwards his only aim was to make ‘action hero’ Narendra Modi the country’s Prime Minister.
"I was asked about fighting Lok Sabha elections from Delhi but I told the leadership that native Patna Saheb is my first, second and last choice," Sinha told reporters at the BJP office here.
Sinha, a supporter of BJP patriarch Lal Krishna Advani, had in the past triggered a controversy by opposing Modi’s name as the prime ministerial candidate.