The man, who was not wearing a life jacket, and a 29-year-old companion were in a small dinghy off the mouth of the Hutt River when they fell into the water just after 5pm.
They were retrieving a fishing net that had been set 20 metres from the shore.
It was "highly recommended'' that anyone in Wellington Harbour in a boat less than 6m long should wear a life jacket, Mr Pickering said.
He urged boaties to look at forecasts and the prevailing conditions before heading out and "make good decisions based on that''.
Police were still contacting family members and unable to release the name of the missing man. They have spoken to his partner, and his boating companion.
It was not known whether the man was an experienced boatie, and there had been no indication he knocked his head when he fell.
Alcohol was not believed to be a factor in the incident, police said.