Sinha is to contest Lok Sabha polls from the Patna Sahib seat.
His supporters attacked those who showed him black flags and beat them up, police officials said.
"Sinha was shown black flags by a group of slogan shouting people opposing his candidature from Patna Sahib. But they were roughed up and beaten up by BJP workers and supporters," said a police official, who was part of police team accompanying Sinha.
Later, Sinha along with his wife Poonam Sinha and his son Luv Sinha filed the nomination papers at the district magistrate's office here.
It was the second consecutive day when Sinha faced protests and black flags were shown to him.
A group of BJP workers opposing his candidature were beaten up by another group of party workers, reportedly supporters of the former actor, Thursday.
Supporters and opponents of the actor-turned-politician, popularly known as "Bihari Babu", clashed in front of the state Bharatiya Janata Party office on Bir Chand Patel Marg here.
Some BJP leaders said there was resentment among party workers after it fielded Sinha, who rarely visits the constituency.
"Not only party workers, the majority of people in Patna are not happy with Shatrughan Sinha," a BJP leader said.