Brys has had a testy relationship with Cameroon Football Federation (FECAFOOT) president Samuel Eto'o since taking the job in April 2024, but his position is funded by the Ministry of Sports and Physical Education.
The coach said in a letter to the ministry, seen by Reuters, that he has made the "decision to unilaterally terminate the said contract for cause, due to the non-payment of my remuneration and that of my staff for more than 60 days."
FECAFOOT said in a statement on Wednesday that they had noted the resignation and would "implement a coordinated response to mitigate the impact of this vacancy at the head of the national team's technical staff."
Cameroon have been drawn in a group with defending champions Ivory Coast, Gabon and Mozambique at the finals of the AFCON, starting in December.
They are currently second in their qualifying pool for next year's World Cup in the United States, Mexico and Canada, a point behind Cape Verde with four rounds remaining. Only the top team automatically earns their place at the finals. The qualification campaign will conclude in September and October.