"We are in the early stages and working through what has occurred," Loughlin added.
He said it was too soon to know what motivated Tom Phillips to take the children away.
Police were speaking with Phillips and the family to understand what went on since the four took off on September 11.
Loughlin said he would not discuss if Phillips was having psychological problems.
"We're speaking to Tom and establishing all the facts about what has occurred."
It was too soon to know even how Phillips and the three children survived so long in the bush.
"They were using a tent. They were in dense bush area."
Phillips was a competent bushman, Loughlin said.
He said it was too soon to say if anybody would face criminal charges.
"Police kept an open mind throughout this investigation."
Jayda Jin, 8, Maverick, 6, and Ember, 5 were all safe and well now, Loughlin added.
A man in the Kiritehere area saw a man on a bike with three children yesterday, and contacted police.
Several search locations of interest - including bush and farmland - were identified.
Police threw everything they had at the search, with aerial surveillance and searches on foot, Loughlin said.
"The search for the family was extensive.
"If you've been out there, that's dense bush area, a significant amount of area we had to cover."
Police searched an area 15km south of where a ute was found, Loughlin said.
The bike sighting was made at about 5.30am yesterday.
That timing sparked suspicion, Loughlin said.
All huts and bush areas were searched to no avail. After these extensive searches, Phillips and the three children turned up at the farm this morning.
Loughlin said police had no contact with Phillips until the father and three children returned to the farm.
Phillips was currently at home, Loughlin said.
"The children are fine. All the appropriate support is being provided to the kids," Loughlin said.
It was still unknown exactly how the four got around the remote, forested areas, and whether anybody else assisted Phillips.
"Our main priority for them is that they're safe and well."
Family members, including the three children's grandparents, were still processing what happened and trying to support one another, Loughlin said.
"This has been really hard on a number of these family members."
The goal of everyone involved - local communities, iwi and police - had been to get Phillips and the three kids home.
"We always held out hope the family was alive."
"It is extraordinary," Loughlin said of the family reappearing.
"To happen this way, is fantastic for the family. This is a family that experienced 17 days of hell, really."
The community went through hell too, Loughlin added.
"We have been greatly supported, I can't speak highly enough of the support we've had."
At one point, it was speculated the family might have been lost at sea.
"We identify and prioritise where we have to go first."
He said whānau and iwi in Kiritehere and Marokopa provided local knowledge and guidance about where to search.
"They're just ecstatic that the family are home."
"We always held out hope that we'd be able to bring the family home alive."
It wasn't even clear if the kids understood what had happened.
"My colleagues have said the kids are happy," Loughlin added.
"They're playing like children do."
Phillips and his three children - Jayda Jin, 8, Maverick, 6, and Ember, 5 - had not been seen since September 11. His ute was found on a nearby beach, facing out to sea.
Police and emergency services - as well as hundreds of locals and volunteers - spent days searching for the family in the area of Kiritehere and Marokopa since Monday, September 13.
Phillips' sister Rozzi Pethybridge told Newshub he "just walked in the door".
"As Dad said, 'I just hope he walks in,' and he has. This is the best-case scenario," said Pethybridge.
"I talked to him for about two minutes and there were lots of tears. I want to be respectful of Tom's wishes so I can't say too much at the moment, but Tom was in a helpless place - he chose a safe place to clear his head."
Tom's mother, Julia Phillips, told the Herald they were "just relieved and really thrilled" that they had returned home.
She said her daughter Rozzi was due to speak on behalf of family tomorrow but they were "absolutely thrilled" they had come home unscathed.
Police are due to release more details this afternoon.
Otorohanga Mayor Max Baxter said there was an "overwhelming sense of relief". He said he was really pleased the three children were safe and sound, but Tom did have a lot of questions to answer.
"There will be mixed emotions on behalf of the family, there's no question. As the communities will have the same mixed emotions. But at the end of the day there will be an overwhelming sense of relief that the kids are safe and sound."
And Baxter told RNZ it had been an extensive search and he commended police for following through on the missing family.
He said he didn't know where the father and children had been, but he was "of the understanding, it is well thought through prior to going bush" so there would be a few questions to be answered.
Waitomo Mayor John Robertson said he was "over the moon" when he was given a heads up by police early this morning that the family had been located safe and well.
"Huge relief and I guess a huge surprise they were found... it's just great, great news really when you think of the children."
Robertson said the children had been on the community's mind for the last three weeks.
"No one knew. We just could not fathom this one so the assumption was they might have been lost at sea."
'Our biggest fear is a rogue wave'
Earlier this month, the children's uncle, Paul Phillips, was getting more and more nervous about finding them alive.
"Our biggest fear is that it's possible that a rogue wave came in and swept them out to sea. Because Tom was an extremely resilient person we're hopeful that Tom has taken the children camping," he said at the time.
"That's something that he was more than capable of, yes, he was a very resilient man, a capable hunter and he knew how to look after himself and knew his way around the bush.
"It's looking more and more likely that it's not the answer we want," Phillips told the Herald last week.
We all just want them home - mother
The children's mother also earlier thanked those who had been involved in the search, including Waikato Police Search and Rescue staff, Waitomo LandSAR, Hamilton LandSAR, Fire and Emergency New Zealand,and Surf Life Saving NZ.
"We also want to thank the air support units who have been helping with the search, the local Iwi and community for their support, and preparation of food donations, any koha given and the families of everyone mentioned for supporting them during their time helping our family.
"We have been incredibly humbled by the generosity and support shown by everyone during this difficult time.
"We all just want Tom, Jayda, Maverick and Ember home."
Just less than a week ago, authorities announced that daily searches for the group would be suspended.
"The family understands police remain committed to bringing their loved ones home, however at this time the daily physical searches will be suspended and we will move into a 'reactive' phase," area commander Will Loughrin said at the time.
"This means police will be available to react to any new information as it comes to hand and initiate searching as required," he said.
Loughrin said at the time the inquiry phase of the operation was still ongoing with investigators continuing to follow-up information as it came in.
He asked anyone who found any items of interest, including clothing, on the coastline areas extending as far north as Papanui Point (near Raglan) and as far south as Waikawau Beach, to contact police.
It was initially thought the family may have been missing at sea after Phillips' vehicle was found at the beach.
The ute was parked facing the sea at Kiritehere beach the day after the family were last seen.
The keys had been put under the mat.
The circumstances of the family's disappearance and exactly how long they have been in Marokopa since being reported missing have not been revealed.
Loughrin said more information would be given at a press conference planned for 3pm today.
