Amarjyoti Kalita was arrested by local police from Lanka area of Varanasi, IG, Law and Order (Varanasi) B P Singh said.
With today's arrest, 14 of the seventeen identified in the incident on the Guwahati-Shillong road on the night of July nine have been taken into custody.
The IG said that Superintendent of Police, Guwahati had informed the state police about Kalita's presence in Varanasi after which he was arrested near Banaras Hindu University.
The identity of Kalita was crossed checked to confirm that the right person was arrested, he said adding that the accused carried reward of Rs one lakh on his arrest.
Assam Director General of Police Jayanta Narayan Choudhury confirmed the arrest.
"Yes the prime accused Kalita have been taken into custody in Varanasi and his interrogation is on," Choudhury told PTI.
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The prime accused was being currently interrogated by a special team of state police in the Varanasi cantonment police station.
Of the 14 arrested, seven are in judicial custody while the cameraman of a local TV who filmed the incident Gaurav Jyoti Nego has been remanded in police custody.
Kalita, a former government employee, was absconding since the incident.