Major Edwin Sumanta recently attended New Zealand's premier military educational institution, the Command and Staff College at Trentham, near Wellington.
Kopassus conducts special operations for the Indonesian government and has been widely accused by human rights groups of violating human rights in Papua and Aceh.
Radio New Zealand International was told by a Defence Force spokesperson that the involvement of Major Sumanta in the college's course is too sensitive for public comment.
The Defence Force says course attendees can be nominated by a New Zealand defence attache.
Separately, the self-proclaimed administration of an independent state of West Papua in May alleged that Indonesian special forces are planning to kill Papua leaders.
These include Papuan leaders who declared a Federal Republic of West Papua at last October's Third Papuan People's Congress in Jayapura, Radio New Zealand International reports.
Five of the West Papuan leadership, including President Forkorus Yaboisembut and Prime Minister Edison Waromi, are serving three-year jail terms for treason as a result of the declaration.
The administration's Foreign Affairs spokesman, Jacob Rumbiak, said their names emerged on a hit-list leaked from a top-level meeting of Kopassus.