A 64-year-old NSW man and 44-year-old Queensland man have been charged following a two-year probe by several police teams in Australia and New Zealand.
Officers opened the case after New Zealand pilot Phillip Mehrtens was kidnapped on a remote Indonesian airstrip by members of the National Liberation Army of West Papua.
He was held captive for almost 600 days before being released in September 2024.
During the investigation of Mr Mehrtens' kidnapping, officers found evidence allegedly linking the two Australian men to the trafficking of firearms to Indonesia.
Both were charged with multiple offences and granted bail before their next appearance in Brisbane Magistrates Court on October 17.
Police allege the men attempted to traffic firearms and ammunition from Australia to the separatist rebel group in West Papua, which is an Indonesian province.
The men also allegedly discussed sourcing Australian military firearms for the paramilitary group.
Australian Federal Police had zero tolerance for any form of violence or gun crime in any nation, Assistant Commissioner Stephen Nutt said.
"Anyone involved in the trafficking of illegal weapons from Australia with the intention of providing them into the hands of international groups should be warned: the AFP and our partners are dedicated to preventing the trafficking of illegal weapons," he said.
"Law enforcement is committed to stopping criminals who facilitate the domestic and international movement of illegal firearms and ammunition.
"The use of these deadly and illegal weapons can have far-reaching consequences if they reach the wrong hands."
The investigation into Mr Mehrtens' kidnapping was complex and required collaboration across multiple jurisdictions, New Zealand Police acting deputy commissioner Mike Pannett said.
"While we are pleased Mr Mehrtens was released and able to return to his family, working closely with the Australian police agencies is an important part of protecting our community here in New Zealand," he said.
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