"Mopping up operations are continuing," said Rarasoa Ralailomady on Sunday, the army's chief spokesperson. "A night operation has not been ruled out but the situation is under control."
Madagascar's paramilitary police and army mounted the assault on Sunday on the renegade troops who staged the mutiny after an officer sent to negotiate with the troops was killed.
Four people were also injured in the ensuing clashes, said Ralailomady.
The mutiny came ahead of a meeting on Wednesday of the Indian Ocean island nation's rival leaders to try to resolve a political crisis that has dragged on since an army-backed coup in 2009.
A diplomatic source said the mutineers' action could be an attempt to derail the landmark face-to-face meeting in the Seychelles between current President Andry Rajoelina and Marc Ravalomanana, whom he ousted in the coup.
Gunfire initially erupted at the Ivatu army base near Antananarivo international airport at 6am (3am GMT) Sunday, lasted four hours and then resumed intermittently.
"This morning there was indeed a mutiny led by certain elements. The chief of staff has things in hand," Defence Minister Andre Lucien Rakotoarimasy said.
"It's going on, we don't know anything about their demands for the moment," he added, refusing to specify the number of renegade troops involved.
Their leader was identified by one source as Koto Mainty, known as the Black Corporal.
The Ivatu base had been the scene of a mutiny in November 2010 amid an attempted coup against Rajoelina.
The failed putsch came as the country prepared to vote in a referendum for a new constitution that would allow Rajoelina, a former disc jockey and once Antananarivo's mayor, to extend his term as head of state.
He has so far failed to steer the country back to democracy.
Soldiers and politics
Soldiers have repeatedly meddled in politics in Madagascar, which gained independence from France in 1960.
Rajoelina and Ravalomanana, who is living in exile in South Africa, signed a roadmap in September 2011 meant to guide Madagascar to new elections, but the deal still has not been fully implemented.
The 15-nation Southern African Development Community has given the rival leaders a July 31 deadline to reach an agreement, ahead of a timeline for legislative and presidential elections to be unveiled on August 1.
In 2010, Ravalomanana was sentenced in absentia for the murders of around 30 demonstrators killed by his presidential guard in 2009 in protests that led to his overthrow.
Ravalomanana was served with a summons last week over a $23-million lawsuit filed by victims of the February 2009 unrest and is expected to appear in a South African court on August 1.
He has twice tried to return to Madagascar, but officials there have both times prevented him and his wife from entering the country. – AFP