Moharram Ali allegedly incited a mob to pelt stones and fire at the Sikhs and had opened fire at Sahastra Pal, a constable who is battling for his life in a city hospital.
Danish, Mohd Irshad, Mohd Abid, Mohd Shahid and Haji Mohammed Irfan have also been arrested for inciting and abetting violence. Violent clashes had erupted between the Sikha and Muslims in Saharanpur last week.
Police said the main accused was behind the gherao at the Qutubsher police station when the two sides were talking out the matter related to a land dispute, in the presence of senior police officials.
The mob gathered outside the police station had gone on a rampage, firing at people, burning shops and vehicles and pelting stones.
Moharram Ali alias Pappu has confessed to inciting the mob, an official told IANS.
Senior Superintendent of Police Rajesh Pandey confirmed the arrest and said raids were being conducted at various places to arrest others guilty of inciting the clashes.
"We have identified the culprits behind the mindless violence through CCTV camera footage and soon they will be brought to justice," the official told IANS.
Gangster Act and the National Security Act (NSA) would be slapped on the people behind the violence, a district official said.
Meanwhile, a curfew continues to be in place but has been relaxed in select areas for five hours.
These places include Janakpuri, Sadar bazaar, Kotwali Nagar and Qutub Sher, Inspector General Amrendra Senger said.
A dispute over a piece of land followed by a court order had triggered off violent clashes in the city. Para-military forces were called in to bring back peace and contain violence.