Six people have died and three are missing after tropical cyclone Felleng raged through Madagascar, the national disaster management agency said Saturday.

"Felleng has gone, it's now 500 kilometres (300 miles) east of (southern) Fort Dauphin. We have accounted for six deaths, three people missing and about 800 people affected in the capital" Antananarivo, Raymond Randriatahina, the agency's executive secretary, told AFP by telephone.

While other parts of the Indian Ocean island were largely spared by the cyclone, Antananarivo, in north-central Madagascar, was particularly affected.

As the waters rose in the Mamba river, many of the capital's homes were flooded as well as several hundred hectares of rice fields, forcing residents to move to tent camps set up by the authorities.

As the cyclone weakened and travelled out to sea, rescue workers on Saturday left the northeastern part of Madagascar and all alerts were lifted.

Felleng had barrelled along the island's eastern and northeastern coast on Wednesday and Thursday, measuring around 400 kilometres (250 miles) in diameter and bringing gusts of up to 250 kilometres an hour.

Madagascar, off the southeastern coast of Africa, is among the world's islands most vulnerable to cyclones. It has seen 45 cyclones and tropical storms in the past decade.

Cyclone Giovanna and tropical storm Irina last year killed 112 people and affected 90,000.