The charges were announced only three days after Andry Rajoelina secured a new term as the African island's president in an election that was boycotted by most opposition leaders.
The two accused were officially charged on Monday with "threatening state security", said Antananarivo prosecutor Narindra Rakotoniaina.
They have been placed in custody until a hearing on January 16.
"Two army colonels tried to unite battalion commanders in the city of Antananarivo with the aim of inciting them to mutiny," Tahina Ravelomanana, head of the Madagascar gendarmerie criminal section, told AFP.
They acted "to contest the election and destabilise power".
Ahead of the election first round on November 16, the two officers offered the equivalent of about $27,500 to several army leaders so that they would incite soldiers to cause trouble, Rakotoniaina said.
The army leaders refused the bribe and reported the two colonels to the chiefs of staff, who ordered an investigation, he added.
Rajoelina was declared winner of the presidential election on Saturday, without a second round required.
About 10 opposition candidates had organised protests in the capital in the weeks leading up to the vote.
They had called on supporters to boycott the vote saying the result had been fixed. They have refused to recognise the result.
Two requests to cancel the result have been made to the constitutional high court which will have to give the official results by December 4.
Madagascar's elections rarely end without controversy. Rajoelina became president a first time in 2009 when Marc Ravalomanana was forced out of power. He won a first election in 2018.
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