A second person had been taken off the same craft earlier in the day for medical attention.
Police, as the lead agency, were working last night with Coastguard and Maritime New Zealand to find the vessel.
A New Zealand Defence Force spokesperson last night said they were also involved in the search and rescue operation.
“Crew on a Royal New Zealand Air Force P-8A are launching an aerial search while Royal New Zealand Navy ship HMNZS Taupō is also in the area after responding to mayday broadcasts earlier this afternoon,” they said.
“The vessel with one person on board has reported becoming lost while en route to Wellington Harbour.”
The Grassroots Trust Rescue Helicopter was also tracked circling the area, while Coastguard said its Wellington team was on standby to help if called upon.