Around 280 children and staff at the high school in Memmingen, Bavaria, locked themselves in their classrooms after they heard a gun being fired in the lobby of the school.
A warning also came over the school's intercom system instructing children not to leave their classrooms until police could get them all out of the building and to the car park of a nearby supermarket, where buses had been arranged to take them to safety.
Police cordoned off the building and surrounding grounds and searched for the 15-year-old pupil who has gone missing. At 4pm they gave the all clear for the school building, but announced that he was missing and they did not know where he was.
Three pupils told the police how the boy had brought two guns into school that day and had seen him holding them in the lobby area.
A helicopter is circling the area and a team of emergency doctors are waiting outside the school, should a confrontation with the pupil turn violent. They do not yet know what kind of guns the pupil may have.
According to reports from regional radio station Bayerische Rundfunk the guns probably belonged to the father of the pupil but police have not confirmed this.