Floods in Mozambique have killed four children as the heaviest rains in over a decade battered the capital of the southeast African country, authorities said Wednesday.

"In Maputo city we have four confirmed deaths," said Rita Almeida, a spokeswoman for the National Disaster Management Agency, adding that all were children.

The national death toll from flooding now stands at six since authorities raised a flood alert last Friday.

Emergency teams set up temporary shelters around the capital after nearly 400 houses collapsed in Tuesday's heavy downpour.

Meteorologist Sergio Buque from Mozambique's weather office (INAM) said "55 millilitres (2 inches) fell within two hours".

"No drainage system could have withstood that," said Buque.

The deluge was the heaviest recorded since devastating floods in 2000 killed 800 people and affected over four million.

Over 14,000 people nationwide have been affected by the latest floods, especially those living in the Zambezi river basin.

Although rainfall has eased off across many parts of the country, more is forecast for next week.

Authorities say they will be closely monitoring flood-prone southern coastal cities including Maputo, Xai Xai and Inhambane.