Madagascar reeled on Wednesday from a double tragedy in which at least 64 people died in a shipwreck, according to an updated toll, while two people remained missing from a helicopter that crashed during a search for survivors.

A wooden vessel -- believed to be a cargo boat not authorised to carry passengers -- came to grief off the island's northeastern coast early on Monday with an estimated 130 people on board.

"Twenty-five bodies were found this morning near Sainte-Marie island, probably due to sea currents, which brings the death total to 64," gendarmerie general Zafisambatra Ravoavy told AFP.

Five children are among the dead, according to the authorities.

Fifty passengers have been rescued, while the search continues for 15 missing.

The vessel had set off from the village of Antseraka, heading for Soanierana-Ivongo, about 100 kilometres (60 miles) to the south.

Initial investigations suggested the vessel's engine had a "technical problem", according to Adrien Fabrice Ratsimbazafy of the River and Maritime Port Agency (APMF).

He said the issue had left the boat vulnerable to the waves and caused it to run aground on a reef, where it took on water.

General Serge Gelle, centre, was one of two survivors from the helicopter crash -- they swam for 12 hours to reach land
General Serge Gelle, centre, was one of two survivors from the helicopter crash -- they swam for 12 hours to reach land AFPTV / Gaelle BORGIA

A maritime official speaking on condition of anonymity said most of the survivors had been on the bridge of the vessel.

Jocelyne Kalou, who manages the Le Fumet hotel at Soanierana-Ivongo, said the local graveyard was "too small to accommodate all the bodies. They are being sent to villages in the surrounding area."

Local mayor Alban Menavolo said he had helped to take 39 bodies by truck to the village, saying most of them were locals and he had known some of them.

"I am very tired -- I am having to shoulder the grief of the entire community. This kind of tragedy is very rare," he said.

Within hours of the disaster, a police helicopter that had set off from the capital Antananarivo with police minister Serge Gelle onboard to help with search and rescue crashed at sea.

Gelle and an officer were thrown out of the craft and survived by swimming for nearly 12 hours to reach land.

They were found separately on Tuesday morning by locals on the beach at Mahambo, around 75 kilometres (75 miles) from the port city of Toamasina.

In a video shared on social media, Gelle, 57, appeared lying exhausted on a beach chair, still in his camouflage uniform.

"My time to die hasn't come yet," he said, expressing his thanks to villagers and local fishermen.

He said he was cold but uninjured.

"I will be able to resume work in 24 hours," he said.

Gelle spent 30 years in the gendarmerie, rising to the rank of general, before joining the government in a reshuffle in August.

Gelle told AFP TV, "We hadn't been expecting (to crash) at all. The helicopter was being buffeted by gusts of wind, and then we fell."

The cause was not "pilot error" or mechanical failure, he said.

"If I'm still alive... it's because we were flying at low altitude -- we didn't fly very high because we were flying low, following the sea," Gelle said.

He added that he had used one of the helicopter's seats "as a lifebuoy."

A fisherman who gave his first name as Zambi told AFP that Gelle was picked up after he had called out for help.

"We set our sails to go and pick him up when we saw him," he said.

Ravoavy said that Gelle "has always had great stamina in sport, and he's kept up this rhythm as minister, just like a thirty-year-old."

"He has nerves of steel," he said.

President Andry Rajoelina has declared Thursday a day of national mourning.