Banning an Indonesian officer from a training course because he was a member of a unit accused of atrocities wouldn't have achieved much, Prime Minister John Key says.
Human rights activists say they were shocked to discover Major Edwin Sumanta of the Kopassus special forces attended a course at the Command and Staff College at Trentham between May and December last year.
That's been confirmed by the Defence Force, and New Zealand's Indonesian Human Rights Committee says Kopassus has a long history of being involved in abuses including massacres in East Timor and the ongoing violence in West Papua.
"It just came as a real blow to us, the thought that we would be training the worst of the worst," spokeswoman Maire Leadbetter told NZ Newswire.
Mr Key says when he last visited Indonesia, President Susilo Yudhoyono was "very clear" about his desire to see human rights recognised in West Papua.
"I think the commitments he gave were the right ones and we support him in trying to make sure people have their human rights protected," he said.
"I don't think that not having that person in New Zealand would achieve a lot."
Ms Leadbetter says New Zealand should suspend defence ties with Indonesia until that country's military has been held accountable for past violations.
The annual 32-week joint command and staff course prepares officers for senior level appointments and includes studies in command leadership and management, international relations and international law and ethics.