Five people died and thousands were affected in the first tropical storm to hit southern Mozambique since 1984, an official said.

Tropical Storm Dando hit the southern African country from Sunday to Tuesday with gusts of up to 120 kilometres (75 miles) per hour and rainfall of over 200 millimeters (7.8 inches).

It has since dissipated, leaving behind destruction and flooding.

"In total the deaths amounted to five people," said Dulce Chilundo, head of the National Emergency Operations Centre.

Three people died in Gaza province and two in neighbouring Maputo province.

"Three people were electrocuted, one person died when a tree fell on their house. Another was swept away when they tried to cross a river," Chilundo told AFP.

In Gaza, Dando flooded 3,766 houses, while 247 were inundated in the capital Maputo.

In three southern provinces 287 classrooms were left without rooftops.

"We are also warning those in flood-prone areas to leave these places in order to avert the repeat of the cataclysmic scenario of 2000," Chilundo said.

Twelve years ago 700 people died and half a million were displaced in the worst floods in the impoverished country's history.

Heavy rains this week have pounded the northern part of neighbouring South Africa, causing a downflow into Mozambique that pushed the Komati, Umbeluzi and Maputo rivers above alert levels, according to the National Water Directorate.

Since Tuesday Mozambique's southern dam Massingir has pushed discharges from 25 cubic meters per second to 5,200 cubic meters per second on Thursday.

According to National Institute of Meteorology (INAM) spokesperson Sergio Buque rainfall would slow down in the south but increase in the centre and north because of a low pressure system over the Mozambique Channel.