A police spokesman in Papua province, Ignatius Benny Adi Prabowo, said authorities were investigating the incident, with police and military personnel sent to the area to locate the pilot and five passengers.
"We cannot send many personnel there because Nduga is a difficult area to reach. We can only go there by plane," he said on Tuesday.
A military spokesman in Papua, Herman Taryaman, said the pilot had been identified as Captain Philip Merthens and it was unclear if the five accompanying passengers had also been abducted.
The plane operated by Susi Air landed safely early on Tuesday morning, before being attacked by rebel fighters, authorities said.
The West Papua National Liberation Army (TPNPB) claimed responsibility for the attack in a statement seen by Reuters, saying the pilot would not be released until the Indonesian government acknowledged the independence of West Papua - which refers to the western side of New Guinea island.
The TPNPB made no mention of the passengers, but said this was the second time the group had taken a hostage. The first incident was in 1996.
Speaking at a news conference in Wellington on Wednesday, NZ Prime Minister Chris Hipkins said that consular support was being provided but declined to provide further details.
"You'll be familiar with the fact that in these kinds of cases, we keep our public comments on that to be a minimum. The New Zealand embassy in Jakarta is leading the New Zealand government's response on this issue," he said.
The Indonesian Foreign Ministry did not immediately respond to requests for comment.
Indonesia's easternmost provinces have been wracked with a low-level battle for independence since the resource-rich region was controversially brought under Indonesian control in a vote overseen by the United Nations in 1969.
The conflict has escalated significantly since 2018, with pro-independence fighters mounting deadlier and more frequent attacks.
The increased intensity of these attacks have been enabled by an improved ability to obtain more weapons, including by raiding and stealing from army posts, cross-border purchases and the illegal sale of government-issued weapons, the Institute for Policy Analysis of Conflict said in a report last year.
Susi Air founder and former fisheries minister Susi Pudjiastuti said on Twitter she was praying for the safety of the pilot and passengers.Â
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