One of Australia's most wanted fugitives, accused of being involved in a multi-million dollar drug syndicate, has been arrested in the Philippines following a two-year manhunt.

The Australian Federal Police have been searching for 44-year-old Markis Scott Turner since September 2015 after he failed to appear for his trial in the Queensland Supreme Court.

Prosecutors have previously claimed the Mackay businessman was the mastermind behind the scheme to smuggle more than 71 kilograms of cocaine from South America to Australia, through syndicates in Melbourne.

In 2016, three Colombian men were jailed for their role in the plan to import cocaine to Queensland.

AFP Assistant Commissioner Neil Gaughan said steps would be taken to extradite Turner to Australia.

"We greatly value the assistance provided by the Philippine National Bureau of Investigation (NBI) in this matter," Assistant Commissioner Gaughan said.

"Our liaison officers have worked closely with the NBI to confirm the location of the man and were permitted to be present when the man was finally arrested.

"This arrest sends a strong message to would-be fugitives — our reach across the globe is second to none and we will use all our contacts and relationships to find you and bring you before a court."

Local news organisations reported Turner was arrested by Philippines National Bureau of Investigation and was living in Davao City under the name Filip Novak.

Last year, the Brisbane Supreme Court heard from Turner's mother Elizabeth Turner that she believed the 44-year-old had taken his own life.

An arrest warrant for Turner was issued in 2015 and $395,000, used to secure his bail was forfeited to the court.