In a Facebook post, a pharmacy spokesperson said the employee was working at the store from Tuesday, August 4 to Friday, August 7.
"Thus contract tracing is currently underway for the period of August 4 to 7," the spokesperson said.
"The store is being professionally deep cleaned this evening.
"In addition, all staff who worked on these days have also been tested and are currently in isolation at their homes awaiting results."
The spokesperson said no customer of the store would be deemed a close contact of the staff member.
"The infected staff member was wearing PPE in accordance with COVID-19 procedures, had taken all hygiene practices in line with the national guidelines on infection control, had minimal contact with the public during these shifts," the spokesperson said.
"Based on our policy of not allowing customers waiting in store for prescriptions, we can confirm that no customer is deemed a “close contact” according to DHHS advice due to periods of under 15 minutes in store.
"However, we encourage anyone who may develop symptoms, no matter how mild, or if you feel unwell to please get tested and isolate.
The spokesperson thanked the community for their messages of support, and said this was a "highly sensitive matter".
"While we are providing you with updates as we can, we would appreciate any questions to be directed to messenger rather than any rumours circulating," the spokesperson said.
"We are committed to being transparent and honest throughout this process and will continue to post updates as required."
The pharmacy was closed Tuesday morning, and will be closed until at least Thursday.
Greater Shepparton has recorded three new active cases of COVID-19, bringing the region's total to 12.
Victoria recorded 331 new cases of COVID-19 on Tuesday, and 19 additional deaths.
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