The body of Mr Atutahi, who was skippering the fibreglass boat, was found yesterday afternoon in the water near Kawau Island.
Mr Stubbs is still missing.
Debris from their 14ft fibreglass boat was found yesterday morning.
Rodney area commander Inspector Mark Fergus said it was not yet known what caused the men to get into trouble.
"At this stage we don't know [what happened the men], we're focusing our efforts more on finding the remaining man," he said this morning.
The search for Mr Stubbs continued this morning, with friends and volunteers joining official searchers.
"Overnight we had our police launch in the area, which conducted a technical search," Mr Fergus said.
"We were using thermal imaging equipment and some underwater sonar, and we'll also be evaluating the data that came out of that search."
The search would be focused in the Kawau Bay area, and teams would be analysing the tides, currents and winds in the area, "and what effect they may possibly have on expanding the search area", Mr Fergus said,
"Conditions again are reasonably favourable, we're experiencing light winds at the moment. It is expected to pick up slightly during the morning, but nothing that should hamper the search."
Police would also be providing support for the missing men's families, he said, who have been holding a vigil at the scene since yesterday.
"It's a very distressing time for them, they're a very tight family, it's a tight community. They're receiving a lot of support and messages of good wishes."
The families of the men held each other and cried when police delivered the grim news. They had been at the beach from morning.
Mr Stubbs' girlfriend, Carissa De Felice, and father Brian kept vigil for most of yesterday, waiting for news.
Missing fisherman Nick Stubbs.
Miss De Felice's father Mark, who was there supporting her, revealed Mr Stubbs could not swim.
He had joined the De Felice family on holidays to Canada and Rarotonga over the past few years.
"In Raro, he was in the water all the time but he couldn't swim," said Mr De Felice. Seeing the faces on everyone [waiting for news] it's just absolutely devastating. The waiting part is unbearable."
Last night he would not be drawn on whether the two men were thought to be wearing life jackets when they went into the water.
Brian Stubbs was not ready to speak about his son last night.
Other relatives of the missing men were also "too raw".
Family and friends of two fisherman walk on the beach at Martin's Bay after one body was recovered and Nick Stubbs still remains missing. Photo / Jason Oxenham
The tragedy comes two days before the start of New Zealand's first Safe Boating Week, a National Pleasure Boat Safety Forum initiative.
The week aims to focus boaties' attention on getting their boats, gear and themselves ready for a safe summer boating season.
The body recovered off Martins Bay was found a day after father and businessman Garry William Pitman, 56, died in a diving accident off North Cape in the Far North.
The body of 5-year-old Jack Dixon, swept to sea by a wave at Mt Maunganui on October 1, is still missing.
Meanwhile, a husband and wife whose boat drifted off as they dived off Ocean Beach, southeast of Whangarei, sparked a rescue operation yesterday evening. The couple made it safely to shore.
