The decision follows a heated exchange between Brys and federation president Samuel Eto’o on Tuesday, the culmination of a stand-off between the pair after the Belgian was appointed by the country’s sports ministry in April, against the wishes of Eto’o.
Brys had been invited for a working session on Tuesday but several of his support staff, also appointed by the sports ministry, were refused entry to the building in Yaounde.
FECAFOOT later called a meeting of its Emergency Committee, who decided to make the change.
The move could put Eto’o on a collision course with the sports ministry, who have so far stood their ground on the appointment of Brys despite opposition from the federation.
Normally, football federations appoint and pay their coaches but in some African countries this is done by the government, especially when federations are short of funds.
Cameroon have four points from their first two qualifiers and next host Cape Verde on June 8 and travel to Angola three days later.
Only the winners of each of the nine six-team groups qualify automatically for the finals in the US, Canada and Mexico.
