The Malagasy Football Federation (FMF) has suspended its French coach Nicolas Dupuis until further notice, without pay.
In a letter to the coach, the FMF said the coach spent "more time [pursuing] commercial interests for personal publicity" than on the team whose "image" had recently "regressed".
As a result, Dupuis was said to have been, the FMF wrote, "neglecting your main role of managing and your duty of supporting Malagasy football".
While the Frenchman - who has yet to comment - is serving his suspension, Eric Rabesandratana will be in charge of the national team as head coach.
The former Paris St-Germain defender will prepare the team for June's opening 2022 World Cup qualifiers at home to Benin before travelling to play Tanzania.
Dupuis was appointed by Madagascar in 2017 and led the team to a maiden appearance at the Africa Cup of Nations two years later.
Madagascar reached the quarter-finals in Egypt in 2019 but failed to qualify the Barea for next year's finals in Cameroon.
A letter sent by the FMF to Dupuis outlined several reasons behind its decision to suspend the coach.
"Following the results of the men's national team in the Afcon qualifiers, the image and prestige of the team have noticeably regressed in the last matches of the competition," the letter stated.
Dupuis last led the team victory in November 2019, four months after Madagascar unexpectedly reached the Nations Cup quarter-finals.
Madagascar's 4-0 defeat in Ethiopia in the penultimate round of qualifying followed by a goalless draw at home to Niger cost the Barea their chance in Cameroon next year.
"You invested more time in your commercial interests for personal publicity and therefore neglecting your main role of managing and your duty of supporting par excellency the Malagasy football.
"Your publicly denigrating the FMF through social media or media outlets caused international football bodies to react, namely Caf and Fifa."
Since January 2019 Dupuis has combined his job with Madagascar with being the sporting director at French fourth-tier side FC Fleury 91.
The BBC contacted Dupuis, who guided Madagascar to a period of unprecedented success in their history, for comment on Friday.