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 were put up at a number of Woolworths stores apologising for the problem.
Social media posts have revealed shoppers are banked up in stores with their trolleys, unable to move. Others said stores were being closed and that they were being turned away.
A woman named Rose, from Hoppers Crossing in Melbourne, told 3AW customers were offered lollies as they were asked to leave.
A national technical outage brought sales to a standstill at the busy Mackay city store this afternoon.
"Shoppers have been told to leave groceries in baskets in the aisle", one customer from Brisbane wrote on Twitter.
"The registers are now back online at all our stores", Woolworths tweeted just after 4.52pm.
"We can confirm that an IT issue impacted registers in our supermarkets for a short period of time this afternoon".
"The registers are now coming back online in our stores".
The spokeswoman did not say what caused the outage.