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He was killed by gunfire while attending a religious festival after being attacked by six gunmen in Dudrakshya village, Rupandehi District, Nepal (near Butwal) about 300 kilometers west of Kathmandu. Maoist rebels perpetrated the killing. The killers descended on the festival in motorcycles at dawn and shot Pokharel nine times as he stood outside the guest house where he was staying.
The Maoists issued a statement condemning Pokharel for "indulging in sexual exploitation, amassing property illegally, misusing the name of Dalits and trying to garner popular support in favour of monarchy".
Nepal"s government in June 2009 announced it would honor him as a "religious martyr".
