Signs were put up at a number of Woolworths stores apologising for the problem.
Others have been told to leave the stores.
Shopper Sharni was among those asked to leave her groceries behind at the Hampton Park store in Melbourne.
A Daily Mercury reporter at the scene said services had just been restored and customers were once again flowing through the registers.
Woolworth's haven't made a statement yet, but they are replying to tweets explaining that registers "are now back online in all of our stores".More news: IMD forecasts normal monsoon this year
"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.
Shortly after 4pm, the issue began affecting all registers across the country.
Reports on Twitter are filtering through that Woolworths stores across the country have been shuttered as a technical issue cripples their scanning systems.
Shoppers have taken to Facebook across Australia to complain about the outage, accusing the supermarket chain of "ruining dinner plans".
Several media outlets have reported that the outage was Australia-wide, and affected all stores, though Woolworths are yet to make a comment.