Gisborne Mayor Rehette Stoltz says it has been a "very stressful and absolutely nerve-wracking" time in the region as the three fishermen now face another night at sea.
The search for the men has been postponed until first light tomorrow, says Maritime New Zealand.
The ship was reported overdue on Monday afternoon. It had three people on-board.
Two of the missing people were spotted by the bulk carrier, African Tiger on Tuesday afternoon, however, due to the severe weather conditions they were unable to be rescued.
The 180-metre-long African Tiger was unable to remain on scene due to the deteriorating weather conditions.
Those on board threw life rings and flotsam into the water in the area where the two men were spotted.
The New Zealand Defence Force's P8 Poseidon also dropped a life raft in the same area.
Swells in the area were getting as high as six metres and winds were gusting up to 50 knots on Tuesday afternoon.
Efforts were made by both boats and aircraft to keep track and rescue the two missing people, said Maritime New Zealand.
However, these attempts were not successful due to high winds and seas, and the people were still in the water.
The severe weather affected rescue efforts significantly.
'Lovely group of men'
Gisborne Mayor Rehette Stoltz told Checkpoint she knew the family of one of the men.
"[They're] a lovely group of men. Everywhere I went today, someone in Gisborne knows someone on that boat.
"We're such a close-knit community and it is heartbreaking."
As a community they were "praying for the safe return of our men", she said.
She was not aware whether the men had a personal locater beacon on them.