Sean Acree, 38, of Mission, Kansas, was arrested Monday and was being held in the Johnson County jail on $250,000 bond.
He is charged with five felony counts, including aggravated indecent liberties with a child and indecent liberties.
A Veterans Affairs spokesman says Acree had been a training sergeant for the VA police but resigned last month. He made his first court appearance on Tuesday and is scheduled for another next week.
It was unclear after business hours Tuesday if Acree had obtained an attorney.