The report says Bacca received Step II Progressive Discipline for the offense.
However, school officials said that because there were criminal charges, Bacca was eventually allowed back in the classroom.
Bacca is currently being held in the Duval County jail without bail.
According to a Jacksonville Sheriff's Office report released Tuesday, the Windy Hill Elementary School teacher showered with a boy more than once while the victim stayed the night at Bacca's home.
The boy told police that Bacca touched his private parts with his hand on more than one occasion, according to the police report.
The boy also told police that Bacca performed oral sex on him more than once, according to the report.
Bacca was Windy Hill's reigning Teacher of the Year. Bacca was also the co-chair of the youth committee at Riverside Presbyterian Church.
"As pastor, my first priority is to my church family, and I am committed to the ministry and mission to which we have been called," W. Stephen Goyer, pastor of Riverside Presbyterian Church, said in a statement. "At this time, we are carefully evaluating the information we have received concerning the allegations brought against Mr. Bacca, and we will be responsive to any questions the investigative team may have. We have no reason to believe that the allegations occurred in or around church-related activities."