Australian Federal Police said the alleged incident happened during a flight from Melbourne to Brisbane on the morning of June 1.
The two women did not know the man 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 law enforcement.
Other passengers and crew were also spoken to as part of the investigation.
The man, 30, was charged with one count of indecent exposure, which has a maximum penalty of one year in prison.
There is no excuse for offensive behaviour particularly on a flight where passengers are confined to limited spaces, AFP Detective Superintendent Anthony Conway said.
"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."
The man will face Brisbane Magistrates Court on Friday.
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