The websites of 13 schools were reported defaced on Wednesday between 3.30pm and 5.00pm, said the Ministry of Education in a statement.
The affected websites were hosted on one server.
"We have referred the matter to the police for investigation and are working to restore the affected websites," said a ministry spokesman.
The affected school websites are:
1. Bukit Timah Primary School
2. Canberra Primary School
3. Compassvale Primary School
4. Greendale Primary School
5. South View Primary School
6. West View Primary School
7. Woodlands Ring Primary School
8. Henderson Secondary School
9. Kent Ridge Secondary School
10. Maris Stella High School
11. Raffles Girls' School
12. St Gabriel's Secondary School
13. St Andrew's Junior College