Togo vs Cameroon 2-0
Fifa said its decision was taken "on account of government interference".
The suspension could prevent Cameroon playing a key World Cup qualifier against Libya on 6 September.
It came on the same day the national side went top of their World Cup qualifying group, because Togo fielded an ineligible player against them.
The results of the 19 June Fecafoot polls were cancelled by the body's own appeals committee after technical complaints from the losing candidates.
Fifa said in a statement: "The Fifa statutes oblige member associations to manage their affairs independently and with no influence from third parties."
The world governing body says it will help set up an emergency committee to run Fecafoot, whose main aim will be to organise and hold elections by 31 March 2014.
The suspension will be lifted once the emergency panel is allowed into Fecafoot's headquarters to carry out their business unhindered.
More immediately the ban could affect club side Coton Sport, who are due to take part in the group stages of the African Champions League which begin on 20 July.
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