He was charged with falsifying documents that allowed the Garuda pilot, Pollycarpus Budi Priyanto, to travel on Munir's flight.
The pilot is serving a 20-year prison sentence for murdering the activist.
Munir's case has drawn widespread international attention and is seen as a test of how far the Indonesian government has reformed since the 1998 end of former president Suharto's government.
Munir provided legal counsel for victims of officially sanctioned violence during Suharto's 32-year rule.
Human rights groups have long accused BIN of involvement in the killing, which it has denied.