A resident, Kamis Gani, 32, said smoke was seen coming from one of the classrooms, prompting villagers to rush and help put out the fire which broke out about 2.30pm.
"I could hear explosions as the glass panels shattered under the heat caused by the fire," he recalled.
"It took us nearly two hours to bring the fire under control and we managed to stop the fire from causing further damage to the pre-school," he said.
"Luckily there were no pupils in the school when it happened because classes start at 7am and end at 12.30pm," he said, adding all of the pupils had gone home much earlier because it was the exam week.
The school, he said, is located near a water village and is about 15 minutes boat ride from Kg Penimbawan with another 10 minutes drive from Tuaran town.
State Education Department Director Datuk Jame Alip said the school, located some 61km from Kota Kinabalu, was built in 1979 and had a total of 21 teachers, five support staff and 247 pupils, adding that a total of 28 pupils will be sitting for their UPSR this year.
He said the fire destroyed Primary Six, Primary Two and Primary Three classrooms, as well as the teachers' room, library, rehabilitation centre and the administration room, while the pre-school was spared from further damage.
He said classes will not be disrupted and that it will be held in the existing school block which was not affected as well as at the village hall and a vacant laboratory.
"We will be sending chairs and tables to the school tomorrow," he said, adding that he has requested for a detailed report from the school on the incident.
Two fire engines, a boat and a utility vehicle manned by 12 personnel and officers from the Tuaran Fire and Rescue Department, led by its Operations Chief Faidzal Wong, went to the scene following a distress call about 3pm.
Barely two weeks ago on May 5, two blocks of SK Tampasak, Kinarut were razed, resulting in damage to four classrooms, the library, Internet Access Centre, textbook storeroom and rehabilitation centres, while two other blocks were not effected.
A school block at SK Simpangan in Kota Marudu was also destroyed in a fire barely nine hours later, where four classrooms, the headmaster's office, senior assistants' offices, clerk office, surau, teachers' toilet, car garage and 120 chairs, among others, were damaged.
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 under the flats parking area.
For SK Gadong, the fire only destroyed the school's administration, resource centre and the sports storerooms.
Other items reported damaged were textbooks, 10 computers and learning equipment.