A rescue operation has been launched to free Kiwi pilot Philip Merthens, who was taken hostage by separatist fighters Papua.

The Jakarta Post reports a team has been deployed for a search and rescue operation, codenamed Peaceful Carstensz, which was launched by the National Police and the Indonesian Military.

Mehrtens was taken hostage on Tuesday while flying a plane for Susi Air carrying five passengers, including a baby, from Mozes Kilangin Airport in Mimika, in Central Papua, to Paro Airport in Nduga.

The area is a highly militarised district with a long history of insurgency in the newly named Highland Papua province, a Papua police spokesman earlier said.

Mehrtens is married to a woman of Indonesian descent and had been living in her home country.

A friend and former colleague earlier told the Herald the Christchurch man has worked for Susi Air for more than five years and spoke fluent Bahasa - Indonesian language.

In a tweet, Susi Air founder Susi Pudjiastuti asked for support and prayed for the pilot’s safety.

Papua separatists with the Susi Air plane piloted by a New Zealander, now a hostage, before they set it alight. Photo / Supplied

The Ministry of Foreign Affairs and Trade (MFAT) also earlier said it was providing consular support to the Merthens’ family and said it wouldn’t comment further because of privacy reasons.

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Prime Minister Chris Hipkins said he had been given preliminary details and said the New Zealand embassy in Indonesia was working to help free Merthens.

West Papua National Liberation Army spokesman Sebby Sambom has threatened to kill the pilot. Photo / Supplied

West Papua National Liberation Army (TPNPB) spokesman Sebby Sambom also earlier confirmed Mehrtens was alive and was being held hostage for the purpose of negotiations with Jakarta.

“If Jakarta is obstinate, then pilot will be executed to death,” Sambom said.

“Later we from the Management of the TPNPB-OPM Central Headquarters will monitor.”

Sambom demanded accountability from Western governments, including New Zealand, for their co-operation with “the military regime in Jakarta”.

West Papua is the name for the western portion of the island of New Guinea.

Sambom earlier told the Australian the group had released the five passengers on the flight before setting the plane on fire.

“We want to convey that we have taken this pilot hostage and brought it to the TPNPB headquarters which is far from the airfield area,” he said, warning police and military not to carry out reprisal sweeps or make civilian arrests in the area.

“This pilot is a citizen of New Zealand. TPNPB considers New Zealand, Australia, Indonesia, America, Europe, all are responsible.”

Conflicts between indigenous Papuans and Indonesian security forces are common in the impoverished Papua region, a former Dutch colony in the western part of New Guinea that is ethnically and culturally distinct from much of Indonesia.

Papua was incorporated into Indonesia in 1969 after a UN-sponsored ballot that was widely seen as a sham. Since then, a low-level insurgency has simmered in the mineral-rich region, which is divided into the Papua and West Papua provinces

- with AP