Elita, which left two people dead and 5,000 homeless when it hit the island a first time on January 28, hit the west coast early on Tuesday and was reported to be moving inland.
The cyclone, or tropical storm, brought with it winds of up to 180 kilometres (110 miles) per hour, said Alain Razafimahazo, head of the local weather office.
There were also fears of flooding, although there were no immediate reports of casualties.
The cyclone was meantime causing high winds over most of Madagascar including the capital Antananarivo, and was expected to move back across the island from east to west during the day, said Razafimahazo.
He added that the strength of the storm meant damage would be inevitable.
The National Meteorology Institute (INAM) in Mozambique, which is separated from Madagascar by the Mozambique Channel, warned Elita could also affect its coastal areas.
INAM said the situation at sea was "very bad", with waves up to six metres (20 feet) high and winds of about 100 kilometres (60 miles) per hour.
It advised sailors and fishermen not to put out to sea.
Lucille Randrianarivelo, the head of the Madagascar national rescue service, said she hoped casualties on the island could be kept low because the authorities had been able to warn the population that the storm was arriving.
"This time people were warned and there are communication and rescue services in place," she told AFP.
But she warned that flooding caused by the storm could have catastrophic effects.
TERRA.WIRE |