Less than two weeks ago the boat was affected by a fault that caused abnormal vibrations, which was identified during an inspection.
Today, a mechanical issue forced the Aratere to take an alternative route.
"Aratere will enter and exit Queen Charlotte Sound through the northern entrance. Hence, we expect the journey to take about 45 minutes longer than scheduled", the Interislander posted on its Twitter account this afternoon.
"We apologise for the inconvenience, and thank you for your patience and understanding."
KiwiRail has been approached for comment.
Chief executive Greg Miller has previously acknowledged the Interislander fleet of three ferries was ageing and more prone to breakdown.
The Kaiarahi ferry requires major repairs to its gearbox after a sudden failure, which is expected to take until at least March.
Last week KiwiRail announced it had leased an additional freight ferry to secure the Cook Strait- a key link in New Zealand's supply chain.
Valentine, which has been working the English Channel, is being leased for an initial 12 months and is due to arrive in December.
"Old ships tend to have mechanical problems and this has been highlighted with the current mechanical issues on Aratere. While she has now resumed service, we know that disruption is bad for us and our customers," Miller said last week.
"Valentine will help mitigate the impact on freight movements across the Cook Strait, in the event of any further unexpected mechanical disruptions."
Earlier this year, KiwiRail and Korean shipyard Hyundai Mipo Dockyard signed a contract for the delivery of two new state-of-the-art Cook Strait ferries.
The first is due to arrive in 2025 and the second in 2026. The contract price for the two ferries is $551 million.
The two rail-enabled ferries will be able to carry nearly double the number of passengers, and commercial and passenger vehicles compared with the current fleet.
