Police have been guarding the French embassy in the capital
The army chief has given Madagascar's rival leaders 72 hours to solve the island nation's political crisis, which has left more than 100 people dead.
"We promise to remain neutral," said General Edmond Rasolomahandry.
He was speaking after a group of soldiers apparently forced the defence minister to resign.
President Marc Ravalomanana has also appealed for an end to the violence and admitted making mistakes during the turmoil that has lasted several weeks.
"We implore all political players, civil society organisations and other parties to reunite immediately to find a solution within the next 72 hours to help the nation out of the current crisis," said Gen Rasolomahandry.
But military spokesman Colonel Henri Michel Marcellin told the BBC the army was not trying to seize power.
"We're just going to put everything in order. Everybody is behind us, the politicians, the army and other members of the security forces, they're all with us," he said.
"It is us, the army, who are in control of the situation."
In a television and radio address on Tuesday, Mr Ravalomanana said he had made mistakes and knew some people were "furious" with him.
"I understand them. I am ready to listen to you. I promise to take steps to find a solution," he said.
Mr Ravalomanana has confirmed he will attend a national conference beginning on Thursday at which he is expected to hold discussions with opposition leader Andry Rajoelina.
The army's ultimatum followed the resignation of Defence Minister Vice-Admiral Mamy Ranaivoniarivo earlier on Tuesday.
The whereabouts of Andry Rajoelina are not clear
He read out a brief letter of resignation to reporters, but later suggested he may have been under pressure to leave his post.
"Perhaps I resigned under threat. I do not like it that Malagasy people are killing each other," he said.
AFP also reported that clashes had broken out between rival factions on the streets of the capital Antananarivo, injuring 19 people.
The whereabouts of Mr Rajoelina are unclear after a French foreign ministry spokesman said he had left the French embassy in Antananarivo.
Frederic Desagneaux told AFP that Mr Rajoelina, a 34-year-old former DJ, was no longer in the French embassy.
He refused to give further details, directing enquiries to the United Nations.
Earlier, hundreds of government supporters had gathered outside the French embassy, demanding that the opposition leader be handed over.
The BBC's Louvassou Rabari in Madagascar says looting has continued for a second day in Antananarivo.
The head of the emergency services, Cornell Rafolohanitrarivo, told AFP that two people were shot dead and 30 injured during fighting and looting in the capital on Monday.