"We have taken power," said Colonel Michael Randrianirina, head of the CAPSAT (Corps d'armée des personnels et des services administratifs et techniques) unit, in a statement read out in front of a government building.
He added that Madagascar's military was dissolving all institutions except the lower house of parliament, which had voted to impeach President Andry Rajoelina just minutes before for desertion of duty.
Earlier on Tuesday, Rajoelina tried to dissolve the National Assembly in a pre-emptive attempt to halt an opposition-led vote to force him out of office over the island nation's spiralling political crisis.
Rajoelina had faced more than two weeks of deadly street clashes, led largely by young Gen-Z demonstrators furious with the ruling elite over crippling water and electricity outages, eventually forcing the 51-year-old leader into hiding.
The decree to dissolve the assembly"shall enter into force immediately upon its publication by radio and/or television broadcast", the presidency said in a statement published on Facebook. Rajoelina, who had defied mounting calls to resign, defended the move in a separate social media post as necessary to"restore order within our nation and strengthen democracy".
Opposition leader Siteny Randrianasoloniaiko said Monday he would vote to impeach Rajoelina for desertion of duty after he fled the country.
Rajoelina, former mayor of the capital Antananarivo, said late Monday he was sheltering in a"safe space" after attempts on his life, without revealing his location.
The protests began on September 25 and reached a pivotal point at the weekend when mutinous soldiers and security forces joined the demonstrators and refused orders to shoot. They joined calls for the president and other government ministers to step down.
Among them were the elite CAPSAT unit, which played a major role in the 2009 coup that first brought Rajoelina to power.
To try to defuse the protests, the president last month sacked his entire government.
Radio France Internationale reported that Rajoelina departed Madagascar aboard a French military plane at the weekend.
