The separatist organisation that has kidnapped a New Zealand pilot has threatened his execution in an alarming new statement shared online this morning.

The pilot, reportedly Captain Philip Mehrtens, was taken hostage last night while flying a plane for Susi Air carrying five passengers, including a baby, yesterday 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 said.

The Ministry of Foreign Affairs and Trade (MFAT) is providing consular support to the pilot’s family and said it wouldn’t comment further because of privacy reasons.

Prime Minister Chris Hipkins said he had been given preliminary details and told RNZ the New Zealand embassy in Indonesia was on the case.

“I’m aware of the case. I don’t have full details of it... I’m aware that the New Zealand embassy is working on the case.”

Local were investigating the incident and police and military personnel had been sent to the area to locate the pilot and five passengers.

In a statement this morning, West Papua National Liberation Army (TPNPB) Spokesman Sebby Sambom confirmed the Kiwi pilot was still alive and was being held hostage for the purpose of negotiations with Jakarta.

West Papua National Liberation Army Spokesman Sebby Sambom. Photo / Supplied

“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.”

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

In a statement on the New Zealand-Indonesian relationship online, MFAT said they work with the Indonesian defence force through activities such as joint officer training, non-combat training, humanitarian operations and at regional forums.

“New Zealand enjoys a strong relationship with Indonesia. As Pacific neighbours, with complementary economies, we are natural partners,” they said.

“Indonesia is an important partner for New Zealand in combatting transnational organised crime, including terrorism, people smuggling, and illegal, unreported and unregulated fishing.”

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 board 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.”

The Susi Air plane landed safely early on Tuesday morning before it was attacked by rebel fighters.

Sambom said the fighters, led by group commander Egianus Kogeya, set fire to the plane and seized its pilot.

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 two provinces, Papua and West Papua.

- with AP