Separatist gunmen attacked Indonesian army troops who were deployed to rescue a New Zealand pilot taken hostage by the rebels in Indonesia’s restive Papua province, leaving at least six dead and about 30 missing, officials said Sunday.

Initial information from army reports said there were about 36 soldiers at a post in the hilly district of Nduga, when attackers from the West Papua Liberation Army, the armed wing of the Free Papua Movement, opened fire on Saturday.

Indonesian military spokesman Rear Admiral Julius Widjojono talks to journalists after the attack. Photo / AP

At least six died and 21 others fled into the jungle, according to the military reports seen by journalists. A military spokesman confirmed only one dead. Nine soldiers were reportedly being held by the rebels.

Papua military spokesperson Col. Herman Taryaman said the soldiers were part of a group that was searching for Phillip Mark Mehrtens, a New Zealand pilot for the Indonesian aviation company Susi Air who was abducted by the rebels in February.

The Susi Air plane that Phillip Mehrtens was piloting being torched by the rebels. Photo / TPNPB

He said authorities were searching for about 30 soldiers.

“It’s still unknown exactly how many Indonesian army troops died and were injured,” Taryaman said. “We are still searching, but heavy rain, foggy weather and a lack of communication have hampered our search and evacuation efforts.”

First Adm. Julius Widjojono, the spokesman for the Indonesian National Armed Forces, or TNI, told a news conference in the capital, Jakarta, that the search operation will be carried out “with maximum force”.

Indonesian military spokesman Rear Admiral Julius Widjojono gestures during a press conference at Indonesia military headquarter in Jakarta. Photo / AP

He said the rebels confronted troops when they tried to comb an area close to the position of the pilot and his abductors. The rebels shot a soldier who fell into a 15m deep ravine, and launched a second attack while troops were getting his body out, Widjojono said. He confirmed only one fatality so far.

Rebel spokesman Sebby Sambom said in a statement that the group’s fighters carried out the attack in revenge for the killing of two rebels in a shootout with Indonesian security forces last month. He said at least nine members of Indonesia’s elite army force were killed in Saturday’s attack.

Sambom urged Indonesia’s government to stop its military operations in Papua. He also said his group had offered to negotiate with both the Indonesian and New Zealand governments for the pilot they took hostage, but said they had not received a response.

“Indonesia’s government must stop its security operation in Papua and be willing to negotiate with our leaders under the mediation of a neutral third party from a United Nations agency,” Sambom said.

Widjojono said the military operations in Papua were launched with a view to avoid a large number of casualties.

“TNI has never stepped back even once in maintaining our territorial sovereignty,” Widjojono said. “And this is being implemented consistently in Papua.”

New Zealand pilot Phillip Mark Mehrtens (third right), was abducted by the independence fighters in Paro in remote Nduga district. Photo / AP

The rebels in February stormed a single-engine plane shortly after it landed on a small runway in Paro in remote Nduga district and abducted its pilot. The plane initially was scheduled to pick up 15 construction workers who had been building a health centre after separatist rebels threatened to kill them.

Saturday’s fighting is the latest in a series of violent incidents in recent years in Papua, a former Dutch colony in the western part of New Guinea that is ethnically and culturally distinct from much of Indonesia. Conflicts between indigenous Papuans and Indonesian security forces are common.

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 region, which is divided into two provinces, Papua and West Papua.

Rebel attacks have spiked in the past year, with dozens of rebels, security forces and civilians killed.

-Alfian Kartono and Niniek Karmini, Associated Press