The school children in the western town of Oelde had built the nuclear reactor mock-up out of a computer casing and taped a "radioactivity warning" they had printed out from the internet on its side.
"When the boys returned to their 'nuclear power plant' from a brief stop at home they were sent away again as the area and a wide radius around it had been cleared and blocked off," police said in a statement.
Residents were ordered not to leave their homes and firefighters tested for a radioactive leak.
The boys' parents thought the fire department was conducting a drill until they read about the operation online and what led to it.
They reported to the police station and explained their six-year-olds had not managed to build an actual nuclear reactor.