Accused Firoz Khan (35) was nabbed by Bihar police from his maternal uncle's home in Hussainabad locality under Muzahidpur police station areas of the district, officer in-charge of the police station Jameel Ashgar told PTI.
Ashgar said the accused was arrested with the help of local residents.
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.
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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.