Rajoelina's statement comes after an elite unit within the military on Saturday joined government-critical demonstrators in the capital Antananarivo who are demanding the president's resignation.
The rebellious unit, Capsat, urged the security forces to "refuse orders to shoot" and condemned the police's attempts to suppress the youth-led protests that have been going on for over two weeks.
On Sunday, Capsat announced that it had taken control of the entire military. Hours later, it was announced that Defense Minister Manantsoa Deramasinjaka Rakotoarivelo had appointed a new army chief – nominated by Capsat.
I gave him my blessing, says the minister, who was appointed by Rajoelina last week.
Unclear situation
"The President's office of the Republic wishes to inform the nation and the international community that an attempt to illegally and violently take power, in contravention of the constitution and democratic principles, is currently underway on the country's territory", it says in a statement from President Rajoelina.
He himself came to power through a coup in 2009 – with decisive help from Capsat.
A spokesperson for Capsat tells AFP that they "responded to the people's cry" but dismisses that it is a coup and blames the president for the chaotic situation.
The newly appointed army chief, General Demosthene Pikulas, does not want to comment on the demands for Rajoelina's resignation, but says that it is now the military's task to restore order.
Regular protests
Demonstrations began at the end of September, against, among other things, poor water and electricity supply in the country. Then, over 20 people were killed and hundreds injured in connection with the protests. On Saturday, when the protests intensified again, two dead and at least 26 injured are reported.
The island nation in the Indian Ocean, which is among the poorest in the world, has regularly experienced extensive popular protests since independence from France in 1960.
