Juan Jose Aguilar, 45, is charged with lewd and lascivious conduct with four children under the age of 14.
Police say much of the abuse occurred in his classroom at lunch or after school. Prosecutors would not say whether any of the alleged victims were students.
Aguilar has been teaching in the Hueneme Elementary School District for more than 15 years. School district officials say he has been placed on unpaid leave.
Parents tell Eyewitness News they were surprised and upset after hearing about the arrest.
"We have been here for 20 years, and all my boys came through this school," said parent Claudio Sandoval, whose wife is a teacher's aide at the elementary school. "It was really a surprise to us to hear about this teacher because he is supposed to be a good person, but you don't know what you are dealing with."
"I am really mad because those kids are so helpless; they can't do anything," said parent Josefina Santos.
"It's sad that you think the people you are trusting your kids with have a dirty little secret," said parent Frank Castro.
Prosecutors say one boy was allegedly abused for more than two years beginning in 2006, and three other boys were allegedly abused for nearly a year beginning in 1999.
Hueneme Elementary School District Assistant Superintendent Deborah DeSmeth released a statement, which reads in part:
"We are shocked and disappointed that these actions may have occurred and are doing our best to cooperate with law enforcement and the district attorney. We are dealing with conduct alleged to have occurred 13 years ago and all of the administrators who were here are gone. When we have more information, we can begin to examine documents from that time in order to determine what was going on."
DeSmeth says the school district has not been able to verify if any of its students were involved because it has not seen the complaint. She says once district officials receive the complaint, they will begin their own investigation.
Aguilar was arrested July 4 and entered a plea of not guilty in court on Tuesday. He remains behind bars with bail set at over $1 million. If convicted of all the charges, Aguilar could be sentenced to 60 years in prison.