Jeffrey S. Barton, the former head of schools at the Army and Navy Academy in Carlsbad, faces 16 felony counts, U-T San Diego reported Thursday.
Police Lt. Marc Reno said bail would be set at $2.1 million.
Barton, 55, had worked at the private school for 18 years before resigning in June as the administrator in charge of academic and residential programs.
The police investigation began in June when a man reported he had been sexually abused by Barton while a student at the school, Reno said in a statement.
Reno did not say how old the students were when the alleged molestation occurred, or where it happened.
The school, founded in 1910, has 300 students in grades seven through 12.
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