A powerful cyclone is set to slam into the southern coast of Mozambique in the early hours of Thursday, bringing flooding, storm surges and high winds, meteorologists have warned.

Severe tropical storm Dineo will deepen into an intense tropical cyclone on Wednesday, packing wind of 166 kilometres (100 miles) an hour, the South African Weather Service said in a statement.

It warned of "torrential rain resulting in widespread flooding" when the cyclone, currently positioned between Mozambique and Madagascar, makes landfall near the city of Inhambane on Thursday.

"Along the southern coastline of Mozambique, strong and damaging winds (are predicted) as well as sea conditions are expected to become very rough," the statement said, forecasting a storm surge centred near Xai Xai city.

It also warned that some villagers could be displaced by flooding in Mozambique, one of the world's poorest countries, and that heavy rains would hit eastern parts of South Africa on Thursday and Friday.

The Mozambique government's emergency response centre issued an alert over the cyclone threat, and advised people to prepare food and water supplies and be ready to seek shelter.

The country has often been battered by flooding and storms.

In 2000, floods claimed at least 800 lives, and more than 100 were killed in 2015.

Scores have already died in the current rainy season, which began in October.

The high death toll in 2000 triggered donor funding for relocations and improvements to water management infrastructure, early warning systems and emergency response resources.