A resident, claimed smoke was seen coming from one of the blocks of the 32-year-old school, prompting villagers to rush out to help put out the fire which broke out at about 1.20pm.
He said there were not many pupils at school when it happened because classes start at 7am and end at 12.40pm.
State Education Department Director Datuk Jame Alip, when contacted, said the school comprised four blocks with a total of 25 teachers and 250 pupils aged between seven and 12.
He said the damaged blocks were where four classrooms, the library, Internet Access Centre, text book storeroom and rehabilitation centres were. Two other blocks were not effected.
The classrooms affected involved a total of 87 pupils from Primary One till Six.
"Two blocks were not effected. Thus, classes will not be disrupted," he said, adding Primary One to Primary Three classes will be held in the morning session, while Primary Four, Five and Six classes will be held during the evening session.
He said his department will be sending chairs and tables to the school in due time.
Personnel from the Penampang and Papar Fire and Rescue Department went to the scene following a distress call.
In March this year, SK Pekan Kiulu in Tuaran and SK Gadong in Beaufort, were destroyed in a fire the same day.
SK Pekan Kiulu lost one block that housed six classes, an administration office and resource centre affecting about 187 pupils in the afternoon fire.
Classes resumed with pupils undergoing lessons under temporary tents placed near the flats parking area.
For SK Gadong, the fire only destroyed the school's administration, resource centre and the sports storerooms, no lessons were cancelled in 11 classrooms.
Other items reported damaged were text books, 10 computers and learning equipment.