Two Australian men will face court next month in Brisbane over supplying weapons to a guerilla campaign by West Papuan separatists.

The charges relate to allegedly trafficking guns to the paramilitary wing of the Free Papua Movement, which seeks to gain independence from Indonesia and establish a sovereign state in the Western New Guinea region following the occupation of their ancestral lands for the past six decades.

The West Papua National Liberation Army kidnapped New Zealand pilot Phillip Mehrtens who landed across an isolated airstrip in February 2023. That action sparked a joint taskforce that was compromised of officers from the ASIO, Australian Federal Police, Queensland Police and New Zealand Police to establish a fresh investigation.

Mr Mehrtens was captured after landing a small aircraft on a remote dirt runway at Paro Airport and was held for 592 days before being released in September 2024.

The West Papua National Liberation Army released several videos and photos of the pilot during his captivity.

The Papuan territory under Indonesian control is currently divided across six provinces.

The liberation movement consists of a disparate group of armed units, each with limited territorial control with no single commander, but also of several non-combatant groups in the territory that conduct demonstrations and protests; and additionally, a small group of political leaders based overseas that raise awareness of issues in the territory while striving for international support for independence.

A spokesperson for the National Liberation Army hit back at "baseless" claims that the men from Australia supplied weapons, in addition to ammunition, to the insurgent group.

"The West Papua National Liberation Army has never received any weapons from an Australian citizen, and also the West Papua National Liberation Army has its own protocol at the National Command," spokesperson Sebby Sambom said in a statement.

"We at the Central Headquarters Management Control have never received any weapons off Australian citizens, so we consider these allegations baseless.

"We have no official knowledge of any weapons assistance from Australian citizens."

Mr Sambom said his paramilitary group wanted "international advocacy support" while also calling for the "immediate release" of the two men.

The men are accused of conspiring to traffic and supply guns with ammunition to the National Liberation Army.

The taskforce claims it uncovered evidence that allegedly links a 64-year-old and a 44-year-old to arms trafficking activities.

Both men arrested face multiple charges of conspiracy to export weapons and firearm parts, for the unlawful supply of weapons and also for possessing a controlled substance.

The 44-year-old, whose charges may see the man serve nearly 11 years in prison, additionally has been charged with possessing explosives without authority.

The 64-year-old is alleged to have travelled to the Papua province and allegedly take an optical rifle scope to meet with members of the paramilitary group between March and April last year.

He could be sentenced up to 55 years, according to the joint taskforce, if found guilty of all the charges.

They were arrested following search warrants on their two homes in November 2024, where police investigators seized several items related to the charges, including 13.6 kilograms of mercury metal for guns and ammunition.

The men were granted bail and are set to appear in Brisbane Magistrates Court on October 17.

AFP Assistant Commissioner Stephen Nutt said the operation sends a clear message to people seeking to profit from illegal trafficking of firearms.

"The use of these deadly and illegal weapons can have far-reaching consequences if they reach the wrong hands," he said.