Victorian Health Minister Jenny Mikakos has told the state's hotel quarantine inquiry she was left completely in the dark on key decisions in the COVID-19 response, with Premier Daniel Andrews hand-picking Health Department Secretary Kym Peake as mission lead reporting directly to him.

Ms Mikakos told the inquiry she was not told her department would have overall control of the hotel quarantine program, which unleashed Victoria's deadly second wave of the virus, and was not involved in the structure of the program.