The outage has also shut down entire stores.
Social media posts indicate stores impacted locally include Walkerston and Caneland Central. At Haymarket in Sydney, customers were told to return in "an hour", according to one tweet for ABC journalist Michael Janda.
A Daily Mercury reporter at the scene said services had just been restored and customers were once again flowing through the registers.
More than 20 shoppers were reportedly turned away by the security guard.
Pictures taken from stores in Sydney and Melbourne show customers waiting at registers with trolleys full of food and groups of abandoned carts. "We apologise for any inconvenience caused".
Shortly after 4pm, the issue began affecting all registers across the country.
Registers temporarily shut down at a number of Woolworths stores across the nation due to a major technical outage this afternoon.
Registers have shut down with stores unable to make sales.
The supermarket giant has taken to Twitter to confirm the IT issue has since been resolved.
News Corp Australia has contacted Woolworths for comment.