The junta named Gomou to serve as acting prime minister on July 17. Officials said Beavogui, who was appointed by the junta a month after it seized power in a coup in September, was receiving medical treatment.
Gomou previously served as commerce and industry minister in the transitional government. His appointment as prime minister was announced in a statement read on national television.
The junta has faced deadly protests in recent weeks over its plans to stay in power for the next three years and is in negotiations with West African neighbours over a possible shortening of that timeline.