The suspension means Chadian clubs and officials are banned from continental competitions.
It puts in doubt Chad's African Nations Championship qualifier against Congo this weekend.
The move also threatens the country's participation in the forthcoming qualifying campaign for the 2010 World Cup and Africa Cup of Nations.
The minister dissolved the executive committee of the federation and created a committee to prepare the organization's general assembly.
Earlier this month, Fifa suspended the Malagasy FA over similar allegations.