In a joint statement released on Wednesday by FMF along with Mexico's premier men's and women's leagues - Liga MX and Liga MX Femenil - officials stated Hernandez's comments violated their gender and diversity policies and amounted to a form of media violence.
A spokesperson for the Chivas Guadalajara player did not promptly respond to a Reuters inquiry for comment.
FMF has imposed a financial penalty and issued a warning, with the possibility of more severe repercussions if Hernandez repeats such actions.
"A few days ago on the social media platform 'TikTok', Hernandez made statements that promote sexist stereotypes considered media violence and contrary to gender equality in sports," the football authorities stated in their announcement.
"The Gender and Diversity Commission has announced that it has started an investigation aimed at preventing and penalizing this behavior, deciding to impose a financial penalty and a warning on Javier 'El Chicharito' Hernandez, stating that this Commission will take more stringent actions if there is a repeat offense."
Hernandez, 37, shared videos over the weekend in which he urged women to "allow themselves to be guided by a man" and accused women of "erasing masculinity."
The prominent athlete also remarked that society had become "overly sensitive" and questioned feminist perspectives on domestic roles.
The comments were met with widespread criticism as sexist and out of touch with modern society, drawing condemnation from fans and public figures, including President Claudia Sheinbaum.
"He's an excellent footballer, but regarding his views on women, I believe he still has much to learn, as women can be whatever we choose to be," Sheinbaum stated during her daily news briefing on Wednesday.
Hernandez, Mexico's all-time leading scorer, returned to his boyhood club Chivas in January 2024 after playing for LA Galaxy and several top European clubs, including Manchester United, West Ham United, Real Madrid and Sevilla.
Chivas also denounced his comments.
"The club has taken appropriate steps in accordance with its internal policies," the Liga MX team stated.
"As an institution with a strong sense of social responsibility, we categorically reject any behavior, stance, or expression that reinforces stereotypes limiting the freedom, respect, and full development of all individuals."