Intense rainfall deluged the capital after a long period of hot and dry weather, with authorities issuing a warning over flooding.

"Kampala today morning experienced intense rainfall leading to severe floods," said Kampala Metropolitan Police deputy spokesman Luke Owoyesigyire.

Seven people, including a three-year-old girl and her 11-month-old sister, had died in the flooding, he told AFP, with a third so-far unidentified boy also perishing in the waters.

Pedestrians were swept away with the city reporting significant property damage, he said.

An employee of the United States embassy in Kampala was among those killed, Owoyesigyire added. The US embassy is yet to comment.

The sisters drowned in their home in the Kampala suburb of Bukoto after their mother, currently in police custody over negligence charges, locked them inside after leaving for her night shift.

Kampala has faced significant flooding previously, with poor planning and over-crowding, encroachment on wetlands and a lack of drainage contributing to the damage.