The ferry ran aground just north of Picton around 10pm on Friday following what Interislander general manager Duncan Roy said was a steering failure.
Roy would not give further details of the failure when he spoke to RNZ about midnight.
"We've started an internal investigation and I don't want to make any assumptions until I get some information back from my team on the ship," he said.
The vessel was carrying out a freight-only voyage and the eight specialist drivers and 39 crew members were not injured.
The Aratere was watertight and would remain in place overnight before being refloated after 8am Saturday on the high tide, Roy said.
The company's fleet has been plagued with issues over the past few years.
It has three ferries: Aratere, which can carry 600 passengers, Kaiarahi, which can carry 500, and Kaitaki, which can carry up to 1400.
Kaitaki was built in 1995, while Aratere and Kaiarahi were both built in 1998.
KiwiRail said the three ferries crossed the Cook Strait a combined total of 4000 times a year, transporting nearly 800,000 passengers and 250,000 cars.
In January 2023, the Kaitaki broke down in the Cook Strait and ended up drifting, resulting in a mayday call.
Tug boats had to escort the ferry, which had 880 people on board, to Wellington.
A report later found the breakdown was partly due to KiwiRail not replacing critical engine parts.
Maritime NZ has since filed a charge against KiwiRail under the Health and Safety at Work Act in relation to the incident. The maximum penalty is $1.5 million.
In March 2023, the Kaitaki was again taken out of service due to gearbox issues, then in August, some passengers had to spend the night aboard after it had to turn back mid-sailing due to problems with its steering.
Earlier this year, all passenger sailings on the Kaiarahi were cancelled for several days due to a mechanical fault.
The Aratere itself lost a poorly fitted propeller during a sailing in 2013.
It was out of action for six months for dry dock repair work in Singapore. During that time, cracks in the shafts that turned its rudders were also found and fixed.
Jim Quinn, KiwiRail chief executive at the time, put the full cost of the breakdown between $20 million and $30m.
That included the loss of passenger, rail freight and commercial vehicle revenue, as well as the hire of a replacement ship from Poland, he said.
"It's not just a cost impact, it's a loss of earnings impact as well."
The Labour government had agreed to part-fund a project to build two new ferries and redevelop the ports, but that was canned by the coalition government in December due to spiralling costs.
The project would still be $1.5 billion in the hole after 2050, documents released to RNZ revealed.
Maritime Union communications officer Victor Billot said he did not know what repairs would need to be made to the Aratere, but he would "hazard a guess that it is something that is more likely to happen with an older ferry than a brand-new one".
The fleet was so old it was often difficult to source equipment and replacement components for the vessels, he said.
Maintenance issues had been an all-too common occurrence for the fleet, he said.
"Obviously we need a solution there for that Cook Strait connection and there isn't one at the moment.
"The idea we can just keep kicking the can down the road with these older vessels, as far as the maritime union is concerned, is not really an option."
RNZ
