Zimbabwe's sports commission installed Charles Westerfall as Zifa chairman, after insisting that the Vincent Pamire-led executive is operating illegally.
In-fighting at Zifa had threatened to seriously affect Zimbabwe's preparations, and the team has not played any friendly matches since booking their first-ever appearance at the Nations Cup finals.
"Fifa and Caf would like to express their strong displeasure regarding events at Zifa, in particular the court order, which blocked the elections planned for 11 October, " the letter began.
Sports commission chairman Anthony Mandiwanza has made it clear that he is prepared to sacrifice Zimbabwe's first-ever Nations Cup appearance in Tunisia in order to carry out needed changes at Zifa.