A statement from the Auckland Council-owned port said no one was ever in any danger but "in different circumstances we believe there could be a safety risk".
The container terminal was now being rejigged for increased manual operations.
The automation project has been under way for five years. Its cost is secret. It is being introduced at the same time as the port is operating a manual container handling operation.
There's no suggestion the port is willing to end the project.
A statement said it was committed to completing automation, asserting again that automating a terminal while continuing to operate "is complex and difficult".
The Herald recently revealed the port would not meet the June-July date for full implementation given by its chief executive Tony Gibson.
That timeline was already well behind schedule.
Container import congestion and unloading delays at the port have for months forced ships to divert to Tauranga and Northland to unload cargoes meant for Auckland. Gibson has resigned and leaves on June 30.
A spokesman said the company was working with the automation project's suppliers.
Customers and stakeholders had been advised of the shutdown.
Auckland Council's planning committee chairman, senior councillor Chris Darby, said confidence in the port was already "rock bottom".
"The port company should come clean and fully disclose the status of its troubled automation programme.
"It looks increasingly like it has crashed on a number of fronts. Importers and exporters deserve to know the real state of play, to enable them to make other plans.
"Ports of Auckland's announcement provides little confidence that a 'go live date' for automation will be any time soon."
The port's statement on the latest issue said it had "taken the decision to temporarily expand manual operations" and "reduce the scale of automated operations".
It did not say automation had been completely shut down, a move it only confirmed after information from stakeholders.
Asked by the Herald if rejigging the terminal to handle more container freight manually could speed up operations, the spokesman said that would be speculative.
Container shipping giant Maersk had the same idea.
"Given the current supply chain disruption and terminal congestion, additional space in the yard could theoretically have a positive impact on operational performance of the port to support the current strong market demand," said Maersk head of Oceania export market My Therese Blank.
"It's too early to comment on the impact of this decision as we are yet to receive additional details from Port of Auckland of the timeline and impact to the terminal and yard operation while the change is being implemented.
"We will continue to closely monitor the situation and make adjustments to our schedules if necessary to minimise supply chain disruption for our customers."
Maritime Union of New Zealand national secretary Craig Harrison said the latest problem was not surprising given all the issues already seen with the project.
"This fundamental stuff shouldn't be happening this far down the track.
"The port has to be 100 per cent honest where it is with this (project). The amount of money that's been spent and is still being spent and it's still not working.
"Phil Goff (Auckland mayor) has to ride in. There's no dividend coming out of the port."
Harrison repeated his earlier concern about retail businesses depending on imports with another Christmas coming up.
"This has the potential to send people out of business."
Last Christmas shipping congestion severely disrupted Auckland retailers' import delivery times.
Until this year the Auckland port was New Zealand's main imports gateway.
It has since surrendered that title to the country's biggest port, NZX-listed Port of Tauranga, also the main export gateway. The current supply chain congestion is also hampering exporters.
