The team was disbanded after poor performances in this month's Indian Ocean Islands Games and a row over allowance payments.
Frank Rajaonarisamba has also replaced Maurice Mosa as coach.
"We already felt the atmosphere in the team was not serene before the team left for the Games," Malagasy Football Federation vice president Doda Andriamiasasoa told the country's L'Express newspaper.
"The players had demanded more money and boycotted training. Such behaviour is unworthy of players called to defend the colours of their country."
The country's Olympic team will now take on the powerful Nigeria in Antananarivo on Sunday, a decision that boosts Nigeria's hopes of catching up Group B leaders Guinea.
Madagascar lie bottom of the group with one point from four games.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.