Wellington's Life Flight rescue helicopter has been searching for the man, a spokesman for the Rescue Coordination Centre said.
He was not wearing a life jacket when he fell into the water, the spokesman said.
The New Zealand Defence Force also joined the search, deploying an Air Force NH90 helicopter to assist.
Air Commodore Tim Walshe, the Air Component Commander, said the helicopter was sent from Ohakea airbase following a request from RCCNZ.
Sealord said it is taking the situation very seriously, co-operating with all search and rescue instructions and is providing support to all of its staff, it said.
The Rescue Coordination Centre was notified about the incident at 11.30am, but the man may have been in the water for up to 50 minutes before this.
Weather conditions are moderate in the search area with a 5-knot wind, 1 metre swell and slight southerly.
The first rescue helicopter was in the early afternoon reported to shortly be running out of fuel and heading home, but the spokesman said it would be replaced at the scene by a second chopper.
In addition to the fishing vessel, the police launch Lady Elizabeth 4 was also approaching the search area earlier, while two nearby vessels had also been directed to assist in the search.
Police were told about the incident at 11.49am, a police spokesman said.
A spokeswoman for Wellington's LifeFlight helicopter confirmed the chopper had been called out on a job but was earlier not yet aware of its destination.