The storm, named Boloeste, would be the first tropical depression to make landfall since the beginning of the December-March cyclone season in the region.
At least 15 people were killed and 63 others went missing when cyclone Ernest hit south Madagascar in January last year.
"This tropical depression will hit the southeast coast of Madagascar near Mananjary town," Newsman Ndimizara, a meterological official told AFP.
Early Saturday, the storm, named Boloeste, was drifting at nine kilometres (5.5 miles) per hour with wind speeds averaging 55 kilometres (34 miles) per hour. It was located some 240 kilometres (150 miles) east of Mananjary.