Separatist rebels in Indonesia's Papua region killed nine army personnel after Jakarta did not respond to a request for negotiations, a rebel spokesperson said on Sunday.

A military spokesperson in Papua, Herman Taryaman, confirmed the Saturday attack but could not confirm the number of soldiers killed as communications were cut due to bad weather.

The West Papua National Liberation Army (TPNPB) abducted a New Zealand pilot in February. The group initially demanded Jakarta recognise the area's independence but this month told Reuters they were prepared to drop that demand and were seeking dialogue.

"We asked the Indonesian and New Zealand governments to free the hostages through peaceful negotiations," rebel spokesperson Sebby Sambom said in a recorded message on Sunday.

"But the Indonesian military and police attacked civilians on March 23. Because of that the TPNPB troops had said they would take revenge and it had already started," Sambom said, adding that fighting was continuing on Sunday.

Herman denied the allegation of a March attack on civilians, saying the security forces were protecting civilians who were chased away by the rebels.

"Efforts to provide assistance and evacuation are still being carried out," Herman said, while asking for prayers for army personnel who are searching for the captured Susi Air pilot, Phillip Mehrtens.

A low-level battle for independence from Indonesia continued for decades in the remote and resource-rich Papua region, with the conflict between armed rebels and security forces intensifying significantly in recent years, analysts say.

Tension has simmered since a controversial 1969 vote supervised by the United Nations that saw the former Dutch territory bought under Indonesian control. (Reuters)