The president announced that sporting activities would be allowed but with an audience of not more than 200 people.
Passengers boarding domestic flights will be required to take a coronavirus test 48 hours before departure and will only be allowed to board if the test in negative.
Only one airport was cleared for international flights beginning this month with strict guidelines in place to prevent the spread of coronavirus.
Mask wearing and social distancing are still mandatory across the country.
Madagascar recorded a spike in virus cases in July forcing the government to reintroduce a lockdown in the capital, Antananarivo.
President Rajoelina had promoted a herbal tonic that he said cured Covid-19 but the World Health Organization has maintained that there is no cure for the disease.
The tonic is now being manufactured in pills and continues to be distributed in the country.