Two BSF personnel and three civilians were killed in the blast that took place on May 9.
Manipur Director General of Police told newsmen here yesterday that the force had been on alert since the blast and acting on intelligence input arrested the five within 24 hours.
The five included the kingpin, who is an active cadre of the proscribed People Revolutionary Party of Kangleipak (PREPAK), the DGP said.
PREPAK, whose main demand is the expulsion of outsiders from Manipur, had claimed responsibility for the blast.
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