The collision happened near the Rugby World Cup fan zone, where St John Ambulance staff had just started their shift.
An officer told the Herald one person was being treated on board but they were not injured.
Just after 6pm the Kea reversed "with a bit of a crunch" and returned to the terminal. Passengers got off and were told to make their way to a different pier for a ferry leaving immediately.
One commuter waiting to get home to Devonport said a crowd of 300-400 people built up before the replacement vessel arrived.
He said a Fullers staff member had told him the delay was due to a vessel breakdown.
He told APNZ there were large holes in the bows of both ferries, high above the waterline - the Kea's on the port bow and the Harbour Cat's on the starboard bow.
A Fullers spokeswoman said the company was assessing the damage this evening and more information would be available tomorrow.
The Auckland Harbourmaster's office said it had not yet been informed of the incident but Fullers had 24 hours to do so.