Coach Grace Nyanwumontu said her team was intimidated by Ghana's 7-0 win team during Wednesday's Africa Cup of Nations qualifiers in Kigali.
"They have girls who we think have male hormones. Girls like guys. Our team was scared. When they got down the pitch they conceded goals because they were afraid."
The Rwandan federation sent a statement to AFP in which it confirmed that the coach "is suspended until further notice, due to the inappropriate choice of style she used after the match between Rwanda and Ghana."
"The statements made by the women's coach about Ghana's players are a violation of the rules and values of football in Rwanda," the federation said.
Nyanawumuntu, who became Rwanda's first professional coach in 2014, was suspended as coach of Kigali in 2017 after allegations of sexual harassment against her by the team's players.
She sued the team for unfair dismissal and won the case, while receiving $47,<> in compensation from the club.
Nyanawomontu was appointed coach of the women's national team in June.