The ministry was expecting testing turnaround times to resume.
"We have asked our IT team to provide further details of why the outage occurred and identify what steps, if any need to be taken to prevent this reoccurring."
Some sites, including the pop-up centre on Māngere's Mascot Ave, resorted to recording information manually to be entered into the system later - ensuring testing could continue but at a much slower pace.
Normally, nurses have been able to use tablets to record and verify people's information through a national database as they come to get tested.
However, without access to the system, they were forced to manually process the information.
About four nurses were performing this task at the Māngere site, taking them away from other duties and slowing testing.
Staff at the Ōtara community testing centre, run by South Seas healthcare, opted to stop testing altogether and wait for the system to come back online.
South Seas Healthcare clinical director Dr Andrew Chan-Mow said the problem was not a new one - the system also dropped out on Thursday.
"When it's on hold, you can't do anything," he said.
He suspected the glitch may have occurred due to high demand with testing across the country ramping up.
However, Chan-Mow said it hadn't been a significant disruption today.
"Thankfully, it's just been for 15-20 minutes at a time but it still pauses the queue."
Even though recording people's information manually would enable testing to continue, Chan-Mow said that would be a "last resort" as the information would still need to be uploaded when the system became accessible.
At a pop-up centre in Māngere East, staff have been largely pleased with the rate of testing - about 250 people per day.
However, they said progress was hindered by a number of factors, including connectivity issues which prevented staff from accessing the registration network for periods of time.
Staff then had to take down people's details manually if they were not registered - another aspect which was delaying testing and resulted in wait times of up to eight hours.
Chan-Mow said people had generally been understanding of the technical issue.
"I must say the general public have been very patient."
At the Mascot Ave site, Māori Wardens were called into help traffic management staff after the latter were copping abuse from people waiting in line.
Despite the technological hiccups, Chan-Mow said his staff had tested record numbers of people, averaging 1000 per day for the past three days.
He couldn't speak more highly of their commitment to the job.
"Those people have been working 12-hour days since Wednesday."
He said most of the testing staff had worked during last year's lockdown so were aware of the effort required.
Large groups of people at Auckland testing sites were also slowing progress.
Staff reported carloads of six to nine people were not uncommon.
The Massey Rd site worked past its 4pm closing time yesterday because of the delays - testing until 6pm.
As a result, a more strict traffic management plan had been put in place to ensure the site wasn't overwhelmed.
However, one security staffer said the 4pm closing time had meant essential workers, who finished work at 5pm, were not being tested.
Those first in line at the Māngere East site had queued since 3.30am.
Those closest to the front of the queue told the Herald they had been waiting for almost five hours.
Māori Wardens were also asked to assist at the site because some traffic management staff had been abused by members of the public.
News of delays comes as the Ministry of Health this afternoon announced 35 new cases of Covid 19: two in Wellington and the remainder in Auckland.
There were no new detections of Covid in the country's wastewater systems.
There are now 334 locations of interest.
