Maisarah Bihar died after the Fire Department rescue boat overturned when evacuating flood victims from a village in the interior Keningau district.
She was in her mother's arms when the rescue boat tipped over after several villagers suddenly stood up in panic when strong currents swept the craft.
Department director Nordin Pauzi said Maisarah was among nine villagers and three firemen in the boat when the incident occurred at Kampung Mempikit at about 10.30am on Thursday.
He said the boat was approaching the area where the villagers were supposed to be relocated when it was hit by strong currents.
"The villagers ignored the firemen's advice to remain seated and stood up, causing the boat to become unstable. All on board were wearing life vests," Nordin added.
He said the firemen managed to pull out the nine villagers from the river, including Maisarah.
"However by that time the little girl had swallowed too much water,"said Nordin, adding that firemen immediately rushed Maisarah and her mother to the Keningau hospital.
He said firemen had complied with all procedures and said they had to deal with factors that were beyond their control, including the sudden force of the water currents.
Sabah Education Department Director Datuk Jame Alip said more than 5,000 students had to skip classes on Thursday because of flooding in their schools.
"The schools will reopen as soon as the situation normalises and the classes the affected students missed will be replaced," he added.