Trujillo said that parents and students are "understandably scared."
"Our thoughts and prayers are with the family and with the child," he said.
Trujillo said the school district was not notified officially about the incident until the next morning, though some officials had heard about it on the news.
Trijullo said that school officials had recently approved a "very costly" security system, but that it had not yet been installed. Security cameras already installed in the school are not believed to be functional, he said, but there were no cameras pointed at the spot where the rape happened.
KGO reported that police were called only after someone who was not at the scene heard people talking about the attack, which was still going on.
Police officers found the girl semi-conscious, curled up near a lunch table.
A Richmond High School student told KGO that the school was not safe at night.
One student, 16-year-old Jennie Steinberg, told the Associated Press that her mother has let her transfer from the school Tuesday.
"It's not safe there at all," she said. "I'm not going back."
Trujillo said 1,688 students attend Richmond High School, which has a banner outside naming it "most improved."
"This is the first time anything like this has ever happened," he said. "It's an isolated incident, a horrible incident."