Nine schools in the eastern city of Leipzig were emailed threats, a police spokesperson said, without giving details of the content of the messages.
"We are taking this very seriously," a police spokeswoman said.
Similar messages were sent around Germany, including to schools in Lower Saxony, Saxony-Anhalt and one in Bavaria, though the full extent remains unclear, broadcaster MDR reported.
The broadcaster also reported that violence has been mentioned in the emails, though MDR noted this information has not been confirmed.
The investigation suggests however that the "threats are not serious," another police spokesman said.
Police sent officers to the schools that were threatened and investigators were searching the premises while students and teachers were told not to leave the site, police said.
In Magdeburg, one school decided to cancel classes for the day and let students leave, affecting more than 900 students, while another school initially asked students to remain inside the building. Before noon, students were again allowed to go outside and classes were allowed to continue.
By the early afternoon, police had given the all-clear to the schools in Leipzig and Magdeburg, MDR reported.