A slow-moving cyclone that unexpectedly turned toward Madagascar has killed 11 people on the island nation as high winds ripped down trees and torrents of water rushed through villages, washing away houses, officials said.

Cyclone Gamane was projected to skim the island that sits in the Indian Ocean east of southern Africa, but changed course and made landfall in the north on Wednesday, the BNGRC national disaster management office said on Thursday morning.

Six people have drowned and five others were killed by collapsing houses or falling trees, authorities said, adding that some 7,000 people on the island were affected by the storm.

The cyclone moved slowly, amplifying its destructive effects.

Video images showed torrents of water rushing through villages and people making human chains in waist-deep water trying to help those trapped in their houses escape the deluge.

Numerous routes and bridges were flooded and cut off.

Its rare to have a cyclone like this. Its movement is nearly stationary, General Elack Andriakaja, director general of the BNRGC, told AFP.

When the system stops in one place, it devastates all the infrastructure. And that has serious consequences for the population. And significant flooding, he added.

The low pressure system was expected to graze the northeast coast of Madagascar but it is a natural phenomenon and there was a change in trajectory and it finally came to hit the Vohemar district at 5:45 am on Wednesday, he said.

Gamane has been reclassified as a tropical storm and was expected to leave the island on Friday afternoon, according to meteorologists.

Cyclone season in southwestern Indian Ocean normally lasts from November to April and sees around a dozen storms each year. (AFP)