Customers began to take to social media at quarter past 4pm to report that they were stuck in lines or told to leave the store while the issue is resolved.
At Haymarket, in Sydney, staff shut the store and were turning people away, telling them to "come back in about an hour".
Signs were put up at a number of Woolworths stores apologising for the problem.
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Grocery shoppers in Australia at the supermarket chain Woolworths, were left stranded at the checkout on Monday, after a systems error forced customers to abandon their items and leave the store.
Social media posts indicate stores impacted locally include Walkerston and Caneland Central.
Registers are now back online, a spokesperson confirmed to The New Daily.
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It is generally contracted from contaminated poultry, meat, eggs and water, and affects the intestinal tract. Hens that are infected with salmonella do not get sick, so there's no way to tell if a chicken is infected.
"This type of incident should not occur and we apologise unreservedly to our customers and store teams for the inconvenience caused", Woolworths Group chief executive Brad Banducci said.
The grocer is yet to confirm the cause of the outage.
Registers have shut down with stores unable to make sales.
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