By the time it reached land the cyclone had been downgraded to a tropical storm but still managed to summon up winds of some 100 kilometers (60 miles) per hour.
Later in the day the storm moved back out to sea, leaving parts of the town of Tulear flooded but no one hurt.
"Parts of Tulear are badly flooded with 50 to 60 centimetres (20 inches) of water...in the town centre we have water up to our waists," said local police chief Rolland Randriamapoinona.
The storm system was earlier expected to miss the Indian Ocean state but changed direction and reached Tsiombe district at around 3:00 pm, meteorologist Hubert Andriamparison said.
It was moving at about 22 kilometers an hour and has gusts of up to 150 kph (90 mph), he said.
In March last year the deadliest cyclone to hit Madagascar claimed 241 lives, according to emergency services.
Madagascar is particularly vulnerable to cyclones between December and March.