Andriarijaona suggested that his predecessor had been removed after "negotiations" among senior officers, a signal that the president, who normally appoints the army chief, was no longer in control of the armed forces.
"Negotiations with the general were completed in the fraternity worthy of the army," Andriarijaona said. "Now all the corps in Madagascar are behind me, and our cohesion has not been affected."
The army has expressed frustration over orders to put down anti-government protests, which to date have claimed more than 100 lives, mostly at the hands of the security forces.
Troops had said on Sunday that they would reject further orders to quell demonstrations, but denied they were staging a mutiny.
The army forced Mamy Ranaivoniarivo, the defence minister, to resign on Tuesday over the issue of putting down demonstrations.
Changes within the military came as Andry Rajoelina, the opposition leader, said he would boycott this week's reconciliation talks.
Augustin Andriamananoro, a spokesman, described it as a "categoric refusal," referring to the two-day conference which was due to start on Thursday.
He said the time was not right for talks and that Church leaders, acting as mediators, lacked the credibility to organise the discussions.
Rajoelina has been locked in a power struggle with Marc Ravalomanana, the president, since the start of the year and has called on him to resign.
Rajoelina, who took refuge for several days in the French embassy after evading arrest, has led a wave of protests against Ravalomanana's rule.
Clashes between pro- and anti-government protesters in the capital earlier in the week have left two dead and almost 50 injured, according to hospital sources.
The US is allowing non-essential staff to leave its embassy and has issued a travel warning over "escalating civil unrest".
Madagascar is one of the world's poorest countries and Rajoelina's criticism of Ravalomanana's economic and social policies has struck a chord with large portions of the population.