Government Railway Police (GRP) has also formed four teams to probe the shocking incident.
"We have constituted four teams to further probe the incident of tying a man from the window of Patliputra Express Train (Patna-Mumbai) on March 25," GRP Superintendent, Bhopal, Awdhesh Goswami said.
An assistant sub-inspector posted with GRP has also been suspended in this regard, Goswami said.
Goswami said the three arrested accused -- Vikki (24), Ravi (25) and Balram (25) -- have been booked under additional sections 342 and 307 of IPC and section 153 of Railway Act.
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The accused, all students from Patna, were arrested on March 25 under sections 323, 294 and 34 of IPC, and later released following a court order.
However, they would be re-arrested soon for the alleged crime, Goswami said.
The youth, Sumit Kacchi (25), was beaten up and tied upside down to a window of a train coach for drinking water from the bottle of a fellow passenger without taking their permission between Jabalpur and Itarsi stations on March 25.
Though the accused were arrested the same day, the incident got public attention after a video of it surfaced.
According to a complaint filed by Kacchi, he had boarded coach S-2 of Patliputra Express (Patna-Mumbai) from his hometown Jabalpur that day.
The accused were so infuriated that they pulled the chain and stopped the train between Jabalpur and Itarsi stations, tied Kacchi's leg to outer side of the window with his head down, beat him and forced him to travel in that position for nearly four hours, eye witnesses said.
At Itarsi, some vendors who got onto the coach released him. But the accused beat him with belts at the Itarsi station too, they said.