Firoz Khan (35) was hiding in Badi Masjid area at his relative's place, Seoni's Superintendent of Police (SP) Mithilesh Shukla told PTI.
Acting on leads, the police zeroed in on Firoz at his relative's residence where he was hiding and arrested him, the SP said.
Initially, the residents of the house tried to mislead the police but later neighbours came forward and virtually pulled him out of the house.
The public allegedly thrashed Khan on the spot, after which the police whisked him away, the SP said.
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Khan had allegedly raped the minor girl on April 17 and later dumped her on a farm land. Her parents found her next morning there and rushed her to Netaji Subhash Chandra Bose Medical College, Jabalpur for treatment.
An MP police team, which is in the state on the lookout for the accused and were today in Supual, has been informed about the arrest and they are on way here, Ashgar added.
The girl is battling for life in a hospital in Nagpur.
After committing the crime, Khan had fled to Bihar.
A joint team of MP and Bihar police were trying to arrest him since Sunday last.
After a search for the accused in Banka failed to yield result, the joint police team visited neighbouring Supual district on Indo-Nepal border tracking mobile phone signals, SP Pushkar Anand told PTI.
The police suspected the accused of trying to flee to Nepal through the porous border and his mobile was found switched off. Luck ran out for him and he was arrested tonight in Bhagalpur.
"The condition of the minor girl is deteriorating," the spokesman of the private hospital in Nagpur's Ramdaspeth area had said.