Acting on a tip-off, state police arrested W Jainta Singh alias Dilip alias Lakapa, a resident of Imphal, from Raxual's area bordering with Nepal in the East Champaran district. Nepali currencies, ATM cards and other documents were seized from him, they said.
Later, he was brought to the city and produced in a CBI court which sent him to a four-day transit remand.
Singh is the prime accused in the killing of a professor of Manipur University in 2010 and had been absconding since then, police said.