The issue started at about 11:30am and was fixed at 12:14pm.
Eftpos company Eftpos Central tweeted just after midday, advising merchants not to try to process ANZ or National cards until the fault had been rectified.
People around the country quickly took to social media to vent their frustration during the fault.
"Almost lunchtime in Welly and EFTPOS seems to be out all over town. Mostly ANZ and National apparently, but both merchants and cards," said Lewis Brown.
Velvet Burger posted a Facebook status at about 11:45am: "ANZ has an outage at the moment which is causing the Grababurger issues.
"The amount of money the banks make, you'd think they'd have it sewn up."
"Eftpos is down in Balclutha and apparently wider Otago. Anyone know why? #cantbuylunch," said Laura Roozendaal on Twitter.