About 650 passengers affected by yesterday's cancellations were accommodated on other sailings, and similar arrangements had been put in place today.
The cancelled passenger services today were the 10.30am sailing from Picton, the 2.30pm sailing from Wellington and the 6.30pm sailing from Picton.
Passengers were transferred to the 8.25am Kaitaki sailing from Wellington, the 1.10pm return sailing from Picton, the 6.25pm Arahura sailing from Wellington, and the 10.25pm sailing from Picton.
Scheduled freight services at 10.30pm and 2.30am have also been cancelled. The 9pm Kaitaki sailing from Wellington will carry affected freight.
Ms Lee yesterday said the issue was not related to the Aratere's recent $54 million revamp, nor the ship's engine problems which put a stop to passenger sailings for more than a week in 2011.
The Aratere is one of three Interislander ferries operated by KiwiRail.