Professor Sutton will step down from his role after four years to take up a new role as director of health and biosecurity at CSIRO, Australia's national science agency.
Department of Health secretary Euan Wallace hailed Prof Sutton as an invaluable leader and thanked him for his work during the public health crisis.
"Since joining the Department in 2011, Professor Sutton has helped to develop a strong and responsive public health team, providing critical health information and advice on a wide variety of issues and emergencies over the years," Prof Wallace said.
"He was appointed Chief Health Officer in 2019 and led Victoria's health response throughout the COVID-19 pandemic, playing a key role in keeping the community safe and informed."
Prof Sutton first joined the Department of Health in 2011 and was appointed Chief Health Officer in 2019.
He became a familiar face during the pandemic, often appearing alongside Premier Daniel Andrews at media conferences.
At times, he was marred by controversy, particularly after Melbourne had one of the world's longest lockdowns, which he maintains was necessary.
In early 2020, he became one of the first government officials in the world to acknowledge the health crisis after tweeting that a pandemic was "very likely, if not inevitable" which drew mixed reactions.
There were also previous reports of a looming resignation amid internal clashes between himself and other health experts over conflicting views around public health orders.
Prof Sutton previously acknowledged failures within the state's contact tracing system during an appearance before a state parliamentary inquiry into the matter.
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