The soldiers had seized the barracks located 10km (6.2 miles) from the capital Antananarivo at dawn 16 hours earlier. It was unclear what their grievances or demands were, but the drama escalated dramatically when they shot and fatally wounded an officer who had been sent in to negotiate with them.
"The situation is under control," General Raphael Ramasy, the defence minister's chief-of-staff told the public television station TVN, Reuters reports.
"Corporal Koto Mainty, alias 'Black', has been killed. The other mutineers gave themselves up or were arrested," Ramasy added. The army said Mainty, the leader of the mutiny, was the ex-bodyguard of a former defence minister.
Four civilians had been arrested, and two mutineers and two members of the security forces had been wounded, Ramasy said.
The island nation has been plagued by political turmoil in the three years since then-opposition leader Andry Rajoelina ousted president Marc Ravalomanana, who has been in self-imposed exile in South Africa since then.
The rival leaders are due to meet for talks next week in the Seychelles, according to an aide to Ravalomanana, but the meeting has not yet been announced officially.
"The mutiny could have an impact on the meeting," said retired General Desire Philippe Ramakavelo, a political scientist and member of a transition council. "It is taking place amid turmoil."
The army said a group of armed soldiers had forced their way into the barracks. "The group fired in the air, blocking all attempts to enter into the barracks," it said.
Soldiers and gendarmes surrounded the barracks and a group of army officers were sent in to negotiate with the rebels, the army said. One of the rebel soldiers then shot a member of the negotiating team, Philibert Ratovonirina, the head of the army's communication service said.
The army then launched its assault.
A Defence Ministry statement said Ivato International airport remained open. "We are working normally as usual. But it is up to the companies to decide on their flights," John Brunelle Razafitsiandraofa, the border police chief told Reuters.
The U.S. embassy in Madagascar said flights in and out of the airport had been suspended, but Britain's Foreign Office said in a travel advisory that the airport had reopened and that flights would resume on Monday.
Madagascar is the world's biggest producer of vanilla.
Famed for its lemurs and rain forests, Madagascar's tourism industry has been badly hit by the political insecurity, and investors eyeing its oil, gold and chrome have also become more wary.
ROADMAP IN PERIL
In September, Madagascar's major political parties signed a road map mediated by the Southern African Development Community (SADC), which confirmed Rajoelina as president, allowed for the unconditional return of Ravalomanana, and paved the way for elections within a year.
Last week, the SADC issued a deadline of July 31 to both leaders to reach a final agreement and implement the roadmap otherwise "the party and/or the parties who are responsible for the failure will be disowned from further participation in the process by the international community".
The election commission had been due to announce an election calendar in the coming days.
Rajoelina led often violent street protests against Ravalomanana and eventually seized power in March 2009 with the help of dissident army officers in what many aid donors considered a coup, prompting them to freeze non-emergency aid.
Ravalomanana was sentenced in absentia to life in prison for the killings of demonstrators by troops in the run-up to his removal. He has tried to return to Madagascar without success.
Rajoelina has said the return of the former leader risked stoking tensions, while a senior Cabinet minister said in September that Ravalomanana would be arrested on arrival if he tried to come back.
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