Dr Clare Looker will be Victoria's next chief health officer as Professor Brett Sutton steps down from the role.

Prof Sutton finished in the role on Friday, with Dr Looker to take over from Saturday for a 12-month term.

Victoria's Department of Health said Dr Looker was an experienced public health physician who had held multiple senior leadership roles since joining its ranks in 2016.

As deputy chief health officer, she helped steer the public response through the COVID-19 pandemic.

Dr Looker has a strong background in public health medicine and has worked in clinical medicine and as an epidemiologist at the London School of Hygiene and Tropical Medicine, the department said.

She was named an "established leader" in the 2022 Victorian public sector women awards.

Prof Sutton, who resigned last month after four years in the state's top health job, will take up a new role as director of health and biosecurity at the CSIRO, Australia's national science agency.

He has said the demands of leading Victoria's COVID-19 response took a toll on him.

Prof Sutton's last day on the job coincided with the department announcing it would no longer issue weekly COVID updates via Twitter.

COVID data will continue to be updated on the department's website.

"We once again thank him for his incredible contribution to Victoria since he started in the role in 2019 and wish him every success in his new position," the Department of Health said in Friday's final COVID update.

Prof Sutton worked 16-hour days for six months at the height of the COVID crisis, dealing with death threats and what he described as a "barrage of lies" on social media.

He was named 2023 Victorian of the Year for leading the state through the pandemic.