The state television announcement said "Commerce and Industry Minister Bernard Gomou has been appointed acting prime minister during the period of absence of Mr. Mohamed Beavogui."
The announcement did not explain why Beavogui was taking a leave of absence or how long he would be absent for.
Beavogui, a former civil servant and expert in agricultural finance, was appointed prime minister last October to preside over a promised transition back to democratic rule following a Sept. 5 coup.
Beavogui has sought to foster dialogue about the transition between Guinea's main political parties and civil society leaders, but talks have been marred by boycotts.
West Africa's main political and economic bloc (ECOWAS) has rejected a three-year transition to elections proposed by Guinea's junta, which has been asked to propose a new timeline by the end of July or face economic sanctions