The decisions come as the LGAs have continued to record new COVID-19 cases.
There are five new cases in Mitchell Shire.
Deputy Chief Health Officer Deb Friedman said a number of factors had gone into deciding to end the lockdown in Geelong and Surf Coast, including that most of the cases in the LGAs were linked to other known cases and that there were no major exposure sites.
"We also look at high testing rates, vaccination rates and also any changes to policy that can limit further growth in the short term, and this includes things like no travel between Melbourne and regional Victoria for construction," she said.
Dr Friedman said Mitchell Shire was next to some LGAs that had the highest rates of COVID-19 anywhere in Australia, making it particularly vulnerable to acquiring cases of the virus.
"And that's what we are seeing regularly, pretty much on a daily basis," she said.
An end date has not been announced for lockdown in Mitchell Shire.
Greater Geelong, Surf Coast LGA and Mitchell Shire were all sent into what was intended to be a snap seven-day lockdown a week ago.