The Madagascan army transferred power to opposition leader Andry Rajoelina during a ceremony attended by journalists on Tuesday.
"We have categorically rejected the (military) authority that (president Marc) Ravalomanana asked us to set up after his resignation," Vice Admiral Hippolyte Rarison Ramaroson said.
"We transfer full powers to Andry Rajoelina, who will oversee the transition," he added.
Ramaroson, who was speaking during a ceremony at a military camp, had been appointed by Ravalomanana to the head of a transitional military authority created to rule the country.
Ravalomanana resigned earlier Tuesday under pressure from the army.
earlier related report
UN chief concerned over Madagascar unrest
UN chief Ban Ki-moon on Tuesday voiced grave concern over the unrest in Madagascar and took note of the resignation of President Marc Ravalomanana.
"The secretary general is gravely concerned about the evolving developments in Madagascar," his press office said in a statement. "He takes note of the resignation of President Ravalomanana."
Ban urged all parties concerned "to act responsibly to ensure stability and a smooth transition through democratic means."
"This peaceful path can only be the result of transitional arrangements arrived at by consensus and enjoying wide support," the UN statement said.
The UN boss also appealed to all concerned, "particularly the police and the army, to ensure the security of the population and work together toward a non-violent resolution of the crisis."
And he insisted that the world body, along with others, remained engaged through its senior political adviser on the ground "to help achieve a peaceful, consensual solution in Madagascar."
Ravalomanana announced in a statement earlier Tuesday that the government was dissolved and that he had transferred his powers and those of the prime minister to a military authority.
The move marked a dramatic victory for Andry Rajoelina, the sacked mayor of Antananarivo who has been leading a months-long push to topple Ravalomanana after seven years as president of the Indian Ocean island.
But Ravalomanana's political opponents have expressed fear that such a transitional authority, tasked with restoring order and organizing elections, could end up under the control of officials loyal to the outgoing regime.
Asked whether the developments in Madagascar, a former French colony, amounted to a coup, France's UN Ambassador Jean-Maurice Ripert replied: "The only thing we know is that the president has resigned and we are not qualifying what is happening."
"We are looking to a constitutional form of transition once the president has departed," he added. "We hope there will be no fighting, no bloodshed and that there will be …a constitutional process to elect a new government."
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