The Belgian, 61, replaced former Liverpool defender Rigobert Song, who was axed in February amid their last-16 exit at the Africa Cup of Nations.
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But not even Fecafoot president Samuel Eto’o knew Brys — formerly boss of OH Leuven — had been appointed by the nation’s sports ministry.
A statement read: “The Cameroon FA has taken note, at the same time as the Cameroonians, of the appointment.
“Fecafoot expresses its great surprise at this act.
“This is contrary to the provisions of Decree No 2014/384 of September 2014 on the operation of national football teams.
“This unilateral decision comes at a time when Fecafoot agreed to carry out the instructions of the president of the republic with a view to achieving a reconciliation favourable to our future.
“Fecafoot intends to provide clarification on this unfortunate situation.”
Song became Cameroon boss in 2022 on the orders of the country’s President, Paul Biya, but his deal finished at the end of February.
He led the them to the 2022 World Cup in Qatar, where they beat five-time champions Brazil but were knocked out at the group stage.
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Earlier this year, Cameroon were knocked out in the last 16 of the 2023 Africa Cup of Nations by eventual finalists Nigeria.
Song’s successor last spent three years in Belgian with OH Leuven before being sacked and retiring.
But he has come out of retirement to accept the job with Cameroon.