Pfister, who was set to sign a deal with the Lions on Monday, was named coach by a sole decision made by Sports Minister Augustin Edjoa.
However, Fecafoot hindered the move as they were frustrated by the minister's decision, which was made without their approval.
Fecafoot shortlisted a number of managers to succeed Dutchman Arie Haan, and Pfister was not one of them.
The list, which was ignored by Edjoa, included Horst Koppel, Artur Jorge, Jean Thissen, Philippe Troussier and Steves Manfred.
Fecafoot's position allows them to rule out Pfister's appointment as the former Zamalek coach will not be recognized by FIFA or CAF without the approval of the Cameroonian federation.
Cameroon will start their CAN 2008 mission by facing holders Egypt in the Group C.