The boat was a chartered vessel carrying approximately 30 passengers. It had left the Viaduct this afternoon.
A Coastguard NZ spokesman said two people on the boat "went overboard". They were then retrieved from the water.
A witness who observed the incident from the shore said the vessel involved was a 15m white launch, and maritime police had spent more than an hour close to the boat.
A Coastguard North Shore vessel was sent to the incident while a second Coastguard vessel towed the vessel back into the harbour.
A police spokeswoman said police and Maritime NZ were working together to understand the circumstances surrounding the incident.
The spokeswoman said victim support was being put in place for the other passengers on the boat.