Australian Federal Police charged the man with two counts of people smuggling on Wednesday after executing search warrants in southeast and central Queensland.
The man was the owner of a central Queensland aviation company who allegedly co-ordinated a network of flights to move the men from NSW to Indonesia, Detective Superintendent Adrian Telfer told reporters in Cairns on Thursday.
The final flight to Indonesia was on November 17, with the aircraft operating as an alleged black flight out of Port Stewart in far north Queensland with its transponder deactivated, he said.
The flight allegedly landed in Merauke, South Papua, where Indonesian officials detained the two pilots - an Australian and an Indonesian - and the two undeclared passengers.
The passengers were allegedly wanted in NSW, one on bail with instructions not to leave the state and the other on outstanding arrest warrants.
The AFP alleged the 43-year-old owner of a Rockhampton aviation company co-ordinated a sophisticated people-smuggling operation to help the fugitives escape from Australia.
That involved co-ordinating charter flight from different companies over a week from NSW to far north Queensland.
The AFP executed search warrants at the man's home on Wednesday.
The people-smuggling charges he faces carry a maximum penalty of 10 years in prison.
The two pilots remain in Indonesia and the AFP has yet to interview them.
The charged aviation company manager is scheduled to face Ipswich Magistrates Court on Thursday.
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