Police said at around 2:30pm that the Heid-Tech school and all its pupils were secure, Südwest Presse reported from the small town near the Bavaria-Baden-Württemberg border.
"There's no reason to be afraid," a police spokesman told the local newspaper. Despite rumours, no-one was killed and "we have the situation in hand."
Police confirmed that they arrested three people who were in possession of weapons.
Investigators are now looking into the circumstances leading to the alert.
It is not year clear whether the three young men who were arrested, one inside the school building and two in the immediate area, were carrying genuine or imitation weapons.
Neither is it known whether they were pupils at the school.
The circumstances of the attack are reminiscent of a group of eight young men who burst into a school in Gelsenkirchen, North Rhine-Westphalia on Monday brandishing blank-firing pistols.
Germany remains on high alert for possible terrorist attacks after Friday's mass shootings and suicide bombings in French capital Paris.
Five people were arrested on Tuesday by police in Aachen, near the Dutch border in connection with the attacks.