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.
Signs have been put up at a number of Woolworths branches apologising for the problem, which has been described as a "system fault".
By 5pm, Woolworths tweeted that all registers were back online and apologised for the outage.
Trolleys abandoned at the Caneland Woolworths registers. "We apologise for any inconvenience caused".
UPDATE 4.50PM: STAFF at Wooloworths Caneland Central are unloading shopping trolleys full of stock abandoned at registers this afternoon.More news: Xiaomi Mi A2 likely to launch in India in May
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Stores temporarily closed in response to the outage.
Shopper Sharni was among those asked to leave her groceries behind at the Hampton Park store in Melbourne.
It's the busiest time of the day for Woolworths, but stores around the country shut their doors on Monday afternoon after a nationwide technical issue completely halted sales.
Registers have shut down with stores unable to make sales.
Social media posts indicate stores impacted locally include Walkerston and Caneland Central.