The father, aged 42, from Great Barrier Island, and his 17-year-old daughter had failed to return from a fishing contest on Friday.
A staff member at the Currach Irish Pub, Moira, was elated at the news.
"Oh my God, that's wonderful," she said, before hanging up to go and tell people the news.
Senior Constable Peter Comerhad earlier this morning said he remained hopeful that the pair were safe and well, saying they could have sheltered up in a bay somewhere.
He said a Coastguard Cessna aircraft had begun a search this morning, the police Eagle helicopter did a shoreline search for any debris and police had discussed with the Air Force if they could provide an aircraft.
The boat, an 8m-long older style white timber launch with a blue canopy, was reported missing from Tryphena on Saturday morning.
Great Barrier Island locals had last night been "gutted" the pair were missing.
Earlier a staff member at the pub said "we're an island community, we're all part of a big family here.
"This is something that affects us all."
Sue Daly, a member of the Great Barrier Local Board, said the news was "ecstatic, absolutely ecstatic".
"The alternative was going to be a horrendous thing for most of the community.
"When you come from an island, it is unlike any suburb. All of us know several hundred people. There is a network of care. Island life is like that," Daly said.
He said it was a "nasty day to be out on a boat" yesterday. Izzy Fordham, chair of the Great Barrier Island Local Board, said everyone had been very concerned.
She said the man was a "great guy" and like most people on the island, a keen fisherman.
There were lots of little bays and nooks and crannies on the west side of the island where the missing boat could find refuge and which the skipper was familiar with, Fordham said.
Senior Constable Kevin Stone with the Auckland Police Maritime Unit said the pair were not technically missing as of Saturday evening, only overdue.
"They're not technically in distress, they're just reported as overdue . . . they haven't put any distress or emergency callout on the vessel themselves.
"The guy, as I understand it, he's a pretty good mariner, he knows the area pretty well."
Stone said it was possible the pair had got their dates mixed up and not realised when they were due back for the end of the competition.
"We're just kind of waiting to see if they show up during the weigh-in period."
The unit went out to search for them in the afternoon, but it was like searching for a needle in a haystack, he said.
remained hopeful the local pair were not actually missing but just overdue, and were waiting to see if they showed up for the fishing competition weigh in.
Great Barrier resident Jeff Cleave said the weather conditions on Friday were terrible.
"It was very hard-blowing from the north, northeast. It was that bad it blew off a section of our roof. The wind was way up," he said.
On Friday, Cleave said, his brother came over from Auckland for a visit with a couple of mates by boat in big seas and he was seasick.
Great Barrier Island is 100km northeast of Auckland. At the 2013 Census it had a population of 939.
A police spokeswoman on Saturday said the boat left Tryphena after a fishing competition on Friday and failed to make contact with friends or family who were expecting a call at 5pm.
"We were notified at 11.45am today that a boat with two people on board was overdue," she said on Saturday.
She said the Auckland police launch was yesterday searching the area around Great Barrier Island in heavy seas.
Coastguard spokeswoman Georgie Smith said police had asked Coastguard to support the search but they were unable to do so because of the weather.
"The severe winds are such that at this stage we are not prepared to put people into the search. The safety of our people is paramount," she said on Saturday.
"Our Coastguard Air patrol has been unable to fly due to the weather conditions. We have volunteers on standby ready to help."
