The 32-year-old Queensland man is accused of being one of two pilots who were part of a plan to transport two passengers wanted in NSW out of the country.
It comes three months after a 43-year-old air charter operator was charged, accused of overseeing a sophisticated operation to help the fugitives escape.
An investigation was launched after the 32-year-old was allegedly among four men - two pilots and two passengers - detained by Indonesian officials in November 2025.
The 32-year-old and an Indonesian man are accused of piloting a plane from Coen to Port Stewart in far north Queensland with the transponder deactivated, operating as a black flight.
The plane allegedly picked up two NSW men at Port Stewart and continued to fly with its transponder deactivated until it was above international waters off the far north coast.
It landed in Merauke, Indonesia, where the pilots and undeclared passengers were detained and the aircraft seized by immigration officials, police said.
One passenger, aged 34, was wanted over two outstanding arrest warrants for kidnapping offences, NSW Police said.
The other, aged 35, was sought on two outstanding arrest warrants including for the supply of a commercial quantity of drugs.
The 32-year-old alleged pilot was deported after being released from detention in Indonesia and was arrested when he arrived at Brisbane airport on Thursday night.
He was charged with two counts of people smuggling, which carries a maximum penalty of 10 years in jail.
The owner of a central Queensland aviation company had been charged in March after being accused of co-ordinating a network of flights to move the fugitives from NSW to Indonesia.
It involved co-ordinating helicopter and fixed-wing flights using different aviation companies over a week to take the men from Orange in NSW to Queensland's far north, police said.
The amount of money involved in funding such a complex operation would be "extensive", Australian Federal Police (AFP) said.
"A black flight involves a light aircraft that logs false or no flight plans, flies at a very low altitude or turns off flight monitoring systems to avoid law enforcement," AFP's Detective Superintendent Adrian Telfer said in a statement on Friday.
"These flights are extremely reckless and anyone taking part is seriously risking their life and those on board."
The 32-year-old alleged pilot was due to appear in Brisbane Magistrates Court on Friday.
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