Madagascar's ousted leader Marc Ravalomanana headed home on Saturday to end his three-year exile, on a flight from Johannesburg to Antananarivo, said an AFP correspondent on the plane.

The South African Airways flight took off from Johannesburg's main airport at 10:12 am (0812 GMT), said the airport authority.

It was was due to land about three hours later in Madagascar, where the head of security for the capital has vowed to arrest him over deadly protests that led to his downfall.

Ravalomanana and his wife were seated in the first row of the medium-sized Avro RJ85 aircraft, where they were acknowledged by the captain.

"I just want to inform you we do have a VIP diplomat on board with us today," the captain announced to the passengers, adding that the couple would be the first to disembark in Anatananarivo.

While the head of security for the capital, General Richard Ravalomanana, said the toppled leader would be arrested on arrival, other top officials on the vast Indian Ocean island have not commented on his return.

As the deposed president checked in for his flight, he said that he was confident of a safe return.

"I have just discussed with the prime minister. He said everything was OK," Ravalomanana told reporters at Johannesburg airport.

Prime Minister Omer Beriziky took office in November, heading a government that was agreed by consensus among Madagascar's main political parties, under a regionally brokered roadmap to steer the nation toward elections this year.