Seventeen people were on board the charter vessel when the wave smashed the cabin as the boat crossed the Raglan Bar.
A man was swept into the sea and was found an hour later.
Police were called to Raglan Harbour around 6.50am on Sunday, they said in a statement.
Police Search and Rescue, Coastguard and a helicopter were all sent to the scene.
The crew of the boat had been fishing when a large wave hit it, police said. The cabin collapsed, and those inside received minor injuries.
The man who went overboard was standing at the back of the boat when the wave hit and was swept away.
He was found a short time later in the water by Coastguard and was taken to hospital for an assessment.
Coastguard rescuer Adam Daniel said the man had an emergency locator beacon secured to his body.
"The fact that he had it tied to him probably also saved his life," Daniel said.
"He wasn't really swimming when we got to him, he had been in the water for about an hour and it's not even 15 degrees so normally you'd be well hypothermic at that point and not able to do much."
Five others on the boat were injured, including the skipper.
Police said Worksafe and Maritime NZ had been notified, and an investigation into the incident was ongoing.
