Crew on the Cook Strait ferry Kaiārahi did not know a passenger was missing until they found his car.
A search is under way for the man , who went overboard from an Interislander ferry overnight. A KiwiRail spokesperson said the incident happened on the Kaiārahi.
Police said they were alerted to the incident about 2.20am on Tuesday.
The Maritime Union said crew on board Kaiārahi were shaken by the incident, and did not know the man was missing until they found his car.
"What flagged the crew was that the car was left on board with the keys inside," the union's Wellington branch secretary Fiona Mansell said.
Mansell said she had spoken to members who were on board the ferry, which she said had gone between Picton and Wellington.
She said crew members searched around the ship for the man, then after checking the CCTV cameras found he had gone overboard.
Mansell said the crew were understandably shaken by the events.
"They're feeling okay, a little bit distressed," she said
She said the union had requested and was ensuring support is available to the crew, with a focus on those who had direct interaction with the passenger.
She said the union was awaiting further information as search and rescue efforts continue,
"This is a shocking event, and our thoughts are first and foremost with the family and loved ones of the individual involved."
Police said while they are trying to locate the person, they were not seeking anyone else in relation to this matter.
Ten volunteers from Coastguard Wellington were searching the area aboard rescue vessels Reremoana and Spirit of Wellington.
Coastguard said it was supporting police and Rescue Coordination Centre NZ who were leading the search operation.
"Our volunteers assembled at base at 7.30am and were on the water at 7.54am."
On Flight Radar, two rescue helicopters were seen flying in a grid-like pattern in the area.
GCH Aviation has confirmed its Nelson/Marlborough rescue helicopter was one of those assisting with the search.
