The President's statement comes after parts of the military on Saturday joined thousands of government-critical demonstrators in the capital Antananarivo and urged the security forces to "refuse orders to shoot", while they condemned the police's attempts to suppress the more than two weeks long youth-led protests.
On Sunday, the rebellious military unit in question, Capsat, claimed to have taken control of the entire military.
"All orders"
From now on, all military orders - whether it concerns land, air or navy - will be issued from Capsat's headquarters, says a group of officers in a video clip according to AFP.
Neither the military leadership nor other units have so far commented on the move.
According to media, the rescue service reported two dead and 26 injured on Saturday, when the protests intensified. Demonstrations began at the end of September, against, among other things, poor water and electricity supply in the country.
Regular protests
"The President's office of the Republic wishes to inform the nation and the international community that an attempt to illegally and violently seize power, in contravention of the Constitution and democratic principles, is currently underway on the country's territory", claims Madagascar's President Rajoelina in a statement.
In late September, over 20 people were killed and 100 injured in connection with the protests.
The island nation in the Indian Ocean, which is among the poorest in the world, has regularly experienced extensive popular protests since independence in 1960.