Police said formal identification was under way but the bodies were believed to be of the fishermen, who were reported missing on Monday.
"Police's thoughts are with their families at this difficult time."
It follows a search and rescue operation which was suspended at 7pm yesterday and was due to resume today.
The boat carrying the three men was reported overdue on Monday afternoon.
Gisborne mayor Rehette Stoltz told Morning Report the news the bodies had been found was heartbreaking.
"Our community is in mourning."
She said her love and thoughts were with the families.
"Everyone is waking up to this news and our community is right behind them."
Stoltz said the region was experiencing some of the worst weather it had seen, which made the search difficult.
Crew on a bulk carrier ship - the African Tiger - spotted two men in rough seas off Māhia Peninsula on Tuesday but could not reach them. Those on board threw life rings and flotsam into the water.
The Defence Force's P8 Poseidon also dropped a life raft in the same area.
Maritime New Zealand suspended the search shortly after 7pm yesterday.
Eastland Helicopter Rescue Trust chairperson Patrick Willock said searchers looking for the missing crew in horrendous conditions yesterday were nothing short of heroic.
A helicopter from the trust had been helping with the search.
Willock said the missing people were well known in local hunting and fishing circles. He knew two of the missing men through family connections, he said.
