"The national federation cannot recognise these appointments made outside any legal and regulatory framework," Eto'o, who is Cameroon's all-time leading goalscorer, said Wednesday in a letter made public.
The federation, known as Fecafoot, said it regretted not being involved "closely, nor remotely" in the selection process for the new coach and his staff.
It said the act goes against a presidential decree relating to the organisation of Cameroon's national football teams, which specifies that Fecafoot is responsible for their management.
The federation said it had not received a response to its list of proposed candidates, expressing its "great surprise" on Wednesday at what it called a "unilateral" decision by the sports ministry to appoint Brys the previous day.
Brys, who has coached a number of clubs in Belgium, the Netherlands and Saudi Arabia, succeeds Rigobert Song, whose contract was not renewed by Eto'o after Cameroon were knocked out in the last 16 of this year's Africa Cup of Nations.
Brys is the third Belgian to take charge of Cameroon. The last was Hugo Broos, who led the country to its fifth AFCON title in 2017.
Cameroon resume their 2026 World Cup qualifying campaign in June. They are currently top of Group D, following a win over Mauritius and an away draw with Libya.
