According to The News Straits Times, an 8-year-old boy had drowned near his home in Kampung Lubak after he had fallen from a bridge.
The first casualty was a 2-year-old girl on Thursday who had drowned after falling in floodwaters from a rescue boat at a plantation in Kampung Mempikit in Keningau.
The incident has been confirmed by the Sabah Fire and Rescue Department.
Although the state had seen a respite from the downpours since yesterday, water levels at rivers remain at dangerous levels with many roads still impassable to traffic.
According to the National Security Council (MKN) website, up until 11.53am on Saturday some 5,453 floods victims from 1,172 families are still seeking shelter at 28 relief centres in Tenom and Beaufort.
The Meteorological Department in a statement said thunderstorms in the waters off Perak, Selangor, Labuan and Sabah are expected to continue today.
It added the condition could cause strong winds of up to 50 kph and choppy seas with waves of up to 3.5 metres high, which is dangerous to small boats.
Similar conditions are also expected to occur in the waters off South Reef, North Reef, Layang-Layang and Sulu.
Residents affected by the floods in Sabah have also turned to Social Media websites to give a picture on how bad the situation is in the state.