About 500 doses of the AstraZeneca vaccine were thrown out at the Bendigo Health Community Vaccination Hub last month.
A Bendigo Health spokesperson said the service had received extra stock from the federal government and vaccinated about 500 people before the vaccine expired.
Bendigo Health then discarded the remaining 500 doses of expired AstraZeneca.
"Following a Australian Technical Advisory Group on Immunisation's recommendation and the federal government's decision on June 18 to limit the AstraZeneca COVID-19 vaccine to over 60s only, Bendigo Health received surplus Commonwealth AstraZeneca vaccine that was due to expire at the end of June," the spokesperson said.
"We vaccinated approximately 500 people with this vaccine before discarding approximately 500 doses of it on the Commonwealth's behalf."
Last week, Bendigo Health hit a milestone in its coronavirus vaccine rollout, passing 100,000 vaccinations..
Of the 100,000 residents vaccinated, about 33,000 received Pfizer and 67,000 received AstraZeneca.
About 12,000 people under 40 have received their first dose of a COVID-19 vaccine from Bendigo Health's 50,000 jabs administered.