Cops used water cannons to disperse the crowd who protested a social media comment by a faculty member.
The Alappuzha South Police station issued notices to the gunman Anil Kumar and security personnel S Sandeep to appear before it on Monday.
Charges including unlawful assembly and obstructing public way have been slapped against him, say reports.
Mamkootathil, who was released from jail on bail over cases related to the Secretariat march a day ago, warned the ruling Left in Kerala over intensifying protest.
The state Youth Congress president was booked for allegedly leading violent attacks during a Secretariat march last month.
Youth Congress State Secretary VT Nihal was injured in the grenade attack by the police.
Today, he would be presented in court for the remand proceedings in relation to the three new cases.
Rahul was booked for allegedly leading violent attacks during a secretariat march in the last month.
In the legal suit, Mamkoottathil said if the Left leader doesn't tender an unconditional apology in a press conference within the next seven days, Rs 1 crore should be paid as compensation.
The state has been witnessing a series of protests after police arrested Youth Congress state president Rahul Mamkoottahil on January 9.