Mr Rajoelina also said 11 other deputies and 14 senators had also tested positive for the virus, the AFP news agency reports.
The government had last week placed one of its main regions, which covers the capital, Antananarivo, back under a strict lockdown following a surge in coronavirus infections.
The lockdown was meant to slow the spread of the virus, authorities explained.
There are 4,578 confirmed cases, and 34 people have died since the virus was first detected on the island in March, according to the World Health Organization.
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