The ship's master shut down power to the vessel's propulsion shafts after they failed to respond to instruments on the bridge, My Flyger said.
Tests were successfully carried out on its ability to travel forwards, backwards and stop, and the vessel had been assisted into the berth by the Wellington pilot.
An investigation had been launched and Interislander will be working with Maritime New Zealand and the Transport Accident Investigation Commission to determine the most appropriate course of action, Mr Flyger said.
Arahura's scheduled departures from Wellington at 10.30am and 6.30pm have been cancelled and passengers and freight were being transferred onto other services.