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"The orders to do this or that came from within our armed forces, not from the fundamentalist people," he says.
The program also claims a key figure behind the formation of terror group Jemaah Islamiah was an Indonesian spy.
Former terrorist Umar Abduh, who is now a researcher and writer, told Dateline Indonesian authorities had a hand in many terror groups.
"There is not a single Islamic group either in the movement or the political groups that is not controlled by (Indonesian) intelligence,"
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