The Indonesian Human Rights Committee says it was shocked to discover a member of Indonesia's special forces unit, Kopassus, has trained with New Zealand's defence force.
Major Edwin Sumanta recently attended New Zealand's premier military educational institution, Staff and Command College at Trentham.
The committee says the acceptance of a Kopassus officer onto an elite training programme marks a new low.
Its spokesperson, Marie Leadbetter, says Kopassus has a long and bloody record of violations - especially in West Papua.
She says the Government is sending the wrong message to the Indonesian authorities.
A Defence Force spokesperson say the involvement of Major Sumanta in the college's course is too sensitive to comment on.