Emergency services were called to Back Beach, Port Chalmers about 2.35pm on Tuesday.
A St John spokesman said two ambulances, a first response unit and a rapid response vehicle with a manager, took three people to Dunedin Hospital.
One had minor injuries and the others had moderate injuries, the spokesman said.
A statement from the Otago Regional Council said the passengers went overboard.
Maritime New Zealand confirmed they would be investigating the incident.
Port to Port Cruises and Wildlife Tours owner-operator Rachel McGregor said her company’s boat was undertaking a wildlife cruise when it was struck unexpectedly by a wave at the harbour entrance.
One injured passenger hurt her back on a rail when she was lurched forward and the other two were taken to hospital as a precaution.
The injured passengers were all cleared to go home soon afterwards.
Ms McGregor had kept in close contact with the passengers to offer support, and had appreciated the messages of support she had received herself — including from the passengers on that particular trip.
She had been operating commercially in Otago Harbour for more than 18 years without incident, including in some very trying conditions.
