Two girls, 6 and 15, died in floods in Soweto on Thursday, Johannesburg emergency services said.

Spokesperson Percy Morokane said the 6-year-old girl was a passenger in one of two vehicles, which along with a bus were trapped on Ncube drive by flood waters.

Her body was recovered by emergency workers.

The body of a 15-year-old girl was found in Zone 10 in Meadowlands.

A 20-day-old baby was still missing, as was a cyclist from Mfulo South.

A joint operational centre was established at the Jabulani fire station and was being manned by Johannesburg emergency services, police and volunteers from the 4-by-4 club.

A search-and-rescue operation was being conducted by the emergency workers and two police helicopters were in the air helping with the operation.

"This was one of the worst thunderstorms in a few years. Sowetans have not seen something like this in a while," Morokane said.

"We are committing all available resources to the new disaster in Soweto. We would like the full co-operation of all Sowetans in this time of dilemma."

Disaster management officers were deployed to Braam Fisher next to Dobsonville where several houses were flooded.

They would assess the needs of the people and provide relief where necessary, Morokane said.

Earlier 40 people were injured after a bus, a minibus and four cars were trapped on a flooded bridge.

They were taken to Chris Hani Baragwanath hospital.

Netcare 911 spokesperson Nick Dollman said the Klip River had burst its banks between Orlando and Dube in Soweto.

Sapa