City Police Chief ACP M. Chandra identified the boy as Mohd Razman bin Hailil, whose address was at Kg Kalansanan, Inanam.
He said a police beat patrolling Jalan Tuaran Bypass was stopped by a vehicle, which was carrying the boy's body, at about 3.55pm.
"The body was then taken to the Queen Elizabeth Hospital II where the cause of death was confirmed to be due to drowning," said Chandra.
Meanwhile, traffic came to a standstill as many locations in the city were hit by flash floods and trees were uprooted during the continuous heavy rain, which began at about 1pm.
Chandra said among the flash flood-hit areas were Jalan UMS in front of 1Borneo, Taman Harington-Jalan Kebajikan, Jalan Kepayan, Jalan Tuaran-Simpang Jalan Likas, Jalan Tuaran Kg Tebobon, Foh Sang, Mile 10, Jalan Teluk Likas, Jalan Kg Ganang, Jalan Mile 2Þ, Penampang and Jalan Saga.
There were several trees uprooted in Jalan Tuaran, Mile 4, and Jalan Bukit Bendera, while a landslide was reported in Kg Kopungit, Kepayan. However, nobody was injured.
He said a total of 81 personnel and four officers were mobilised to assist, prevent crime and ensure smooth traffic flow.
"We were also assisted by City Hall, Fire and Rescue Department, Sabah Electricity Sdn Bhd and Telekom," he said, adding that flash floods in many locations receded by 6.30pm.
In Penampang, several areas, including Donggongon town, were also hit by flash floods and a landslide was reported in Kg Limbanak where several graves at the St. Aloysius Church cemetery were damaged.
A villager, who declined to be named, claimed that the landslide unearthed one coffin and damaged 10 graves.
He said the landslide caused the soil to slide between 20 and 30 feet down the hilly slope onto the road junction heading towards the cemetery.
Also affected were several elderly residents of Lido Centre who had to be rescued by police and Fire and Rescue team.
Lido Kapitan Chong Kiam Fah, who was also at the scene to assist, said the water level started rising very quickly and he alerted the police when the water reached knee level.
Chong applauded the rescue teams' prompt action, adding that all those rescued were taken to higher ground and are safe.