The man is accused of entering a female cadet's room on May 6 and committing acts of indecency upon her, ACT police say.
He was arrested on Sunday and charged with two counts of acts of indecency.
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The man was bailed to appear in the ACT Magistrates Court on Tuesday.
In a statement, the Department of Defence said ADFA referred the matter to ACT police and notified the defence force investigative service as soon as the allegations were raised.
"The Australian Defence Force and the Australian Defence Force Academy take such allegations very seriously," the department said.
"The safety and wellbeing of cadets at ADFA is our priority. We have offered full support to all parties involved in this matter."
The charges follow a scandal that engulfed the academy in 2011 when footage of a male cadet engaging in consensual sex with a female cadet was streamed via Skype without her knowledge to a group of cadets in another room.
The incident sparked a series of inquiries into defence misconduct that turned into a political row.
