The march was taken out on September 12 in the recently renovated 'Mittayi Thiravu' (sweet street), despite a prohibitory order being in force in the area.
Despite being told not to take out the march, the actor and the others flouted rules and did so, police said Sunday.
The case was registered under various sections of the Indian Penal Code, including unlawful assembly, breach of peace, rioting and obstructing public way, police said.
Reacting to the development, Joy Mathew said he had taken out the march to express solidarity with the protesting nuns.
"This is an attempt to scare me for supporting the nuns', he said.
The actor said he was not told by police about the prohibitory order in the area.
"We took out a silent march with placards', he told television channels.
Joy Mathew is best known for playing the lead role in John Abraham's 1986 film 'Amma Ariyan', which was voted as one of the Top 10 Indian films by the British Film Institute.
Some of his other films are 'Annyaum Rasoolam', 'Shutter', 'Amen' and 'Honey Bee'.
The nun, in her complaint to Kottayam police in June, had alleged that Bishop Mulakkal raped her at a guest house in Kuravilangad in May 2014 and later sexually exploited her on several occasions.
The nun had said she had to approach the police as church authorities did not act on her repeated complaints against the clergyman.
However, the bishop has denied the charges.