Ulaiasi Uto Viladai, 30, is accused of exposing himself on a Jetstar flight from Melbourne to Brisbane on the morning of June 1.
The two women did not know Viladai and were moved to different seats after they raised the alarm.
He was monitored by cabin crew for the rest of the flight before being escorted off the plane by police.
Other passengers and crew were also spoken to as part of the investigation.
Viladai was charged with one count of indecent exposure, which has a maximum penalty of one year in prison.
Court documents reveal Viladai is residing in Australia on a work visa.
He faced Brisbane Magistrates Court on Friday, where the matter was adjourned until August 15.
Viladai left court quickly after his appearance.
AFP Detective Superintendent Anthony Conway earlier criticised the "offensive behaviour" where passengers were confined in a small space.
"Indecent conduct on a plane will not be tolerated," he said.
"The AFP will take action against individuals who engage in this kind of criminal behaviour."
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