Colonel Michael Randrianirina, interim leader since the former president fled in October after weeks of demonstrations, was to meet Putin on Thursday, it said.
It was one of Randrianirina's first international trips as interim president after the United Arab Emirates and South Africa, where he met President Cyril Ramaphosa in January.
Before leaving the Indian Ocean island, Randrianirina told reporters he had been invited by Russian authorities who had chartered the plane to take him there.
"It's not about choosing our partners based on countries, but about maintaining relations with any state that we believe can bring benefits to the Malagasy people," he said.
Randrianirina became president just days after his CAPSAT army unit took power and ex-president Andry Rajoelina fled on a French military aircraft. He has pledged new elections within two years.
Last month Russian military instructors visited the island to train their counterparts in military equipment supplied by Moscow, including kamikaze drones.
The delegation was led by the deputy head of Russian military intelligence, Andrei Averyanov, the National Assembly president told AFP.
Averyanov is also the alleged supervisor of Russia's paramilitary Africa Corps that succeeded the Wagner group.
Russia, through its embassy in Madagascar, also announced on Wednesday the delivery of a helicopter and trucks to support rescue operations after Cyclone Gezani claimed 59 lives on the island last week.
After Moscow, Randrianirina was due to travel to France, where he could meet President Emmanuel Macron, Africa Intelligence news site said.
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