A Baltimore County grand jury charged William Kern, 46, with misdemeanor counts of second-degree assault and reckless endangerment stemming from the early February incident.
Raymond Gray, a University of Maryland police recruit, was training with city officers at an abandoned psychiatric hospital, when Kern shot him in the head. Kern has said he thought he was firing Simunition rounds after drawing his service pistol.
Gray was released from trauma care 10 days after the incident but remains non-communicative.
Other officers involved with the incident have been suspended as the Baltimore Police Department completes an internal probe. City police have said top commanders were not aware of the training.