Military efforts to find the two missing crew members were called off around 3:45 p.m., about 10 hours after the boat issued a distress call after heading out to sea offshore of Tabusintac.
Mike Bonin, spokesman for the Joint Rescue Co-ordination Centre in Halifax, said two Canadian Coast Guard vessels and a Cormorant helicopter from Greenwood, N.S., had done all they could to locate the two remaining crew members.
"Despite our best efforts, an exhaustive search and after repeating the search pattern area several time, unfortunately there was nothing more that we could do to find these people," said Bonin from Halifax on Saturday.
Bonin said the matter had been turned over to the RCMP.
A few hours earlier around 1:15 p.m., one fisherman, a 23-year-old man from nearby Tracadie-Sheila, was found dead near where the boat hit a sandbar in rough seas and began taking on water, RCMP said.
Spokeswoman Cpl. Chantal Farrah said the case was considered a missing persons investigation.
Farrah said RCMP officers, Tri-County Ground Search and Rescue and teams from Miramichi and Restigouche, as well as local fishermen and residents were combing the shoreline for any sign of the two crew members Saturday evening.
"This is very difficult for all the families involved and we appreciate the efforts from the entire community, who really came together today to help search for the missing men," said Farrah.
Farrah said officials would continue scouring Saturday until there was not enough visibility.
The Transportation Safety Board indicated Saturday it was dispatching a team to investigate the tragedy.
The fishing boat was about five kilometres offshore of Tabusintac, about 50 kilometres northeast of Miramichi, when it sent out mayday call at about 5:30 a.m.
The crew members were last seen standing on the hull of the vessel and were not wearing life jackets, said Bonin.
Their vessel was spotted washed up on the sandbar shortly after the distress call came in and was still visible, he said.
Environment Canada said the water temperature off the south coast of the Acadian Peninsula was between 2 C and 4 C on Saturday.
A New Brunswick Conservative politician said the captain of the vessel had rented it after his fishing boat was destroyed in a fire earlier this month.
Serge Robichaud, who represents the Miramichi Bay-Neguac area in the legislature, said the captain's boat was one of five vessels that were gutted by a blaze at the Tabusintac Wharf on May 5.
He said the community was in mourning and there was still hope among residents that the remaining two fishermen would be found safe.
"This is a small community," said Robichaud from the Miramichi area on Saturday. "It's a tough job, to be a fisherman. Rain or shine, you still need to go and I guess this morning when they left they were at the wharf early and it was rough.
"It's a very sad day."