The 39-year-old's body was discovered in the chopper wreckage at the bottom of Lake Wanaka, two days after the crash.
It is understood Nick Wallis was flying a leased Hughes 500 also carrying two Department of Conservation staff when it crashed today. An empty DoC vehicle can be seen at the airport car park.
Prime Minister Jacinda Ardern has expressed their sympathies for families, colleagues and friends of those who were killed in the crash.
"My heart goes out to the families and loved ones of all those who died in today's tragic crash," Ardern said.
"DOC staff go to work every day on our behalf to take care of New Zealand's precious environment. Their work can take them into dangerous situations.
"It's an absolute tragedy that these staff and the helicopter pilot, who were just going about their work, will never return home."
Conservation Minister Eugenie Sage also expressed her condolences to the families and friends of those killed in the incident.
"This is a devastating tragedy. My thoughts and sympathies are with the families and work colleagues of the two DOC staff members and the helicopter pilot," Sage said.
"I know that DOC is supporting the families and the work colleagues struck by this tragedy. Director General Lou Sanson has flown south to be of assistance and I will be doing the same to offer what support I can."
Inspector Olaf Jensen said the victims' families have been notified and police are working to support them.
"We acknowledge this is the second helicopter crash in the Wanaka area in recent times and the impact this will have on the local community," he said.
The scene will be secured overnight and police are working with other agencies on scene examination and recovery of the victims' bodies.
A former DOC worker who has flown with Nick Wallis on many occasions said it was a brand new Hughes 500 helicopter that was super safe.
"It will be really interesting to find out what has happened here. I can't believe it would a pilot error as Nick was super experienced and a really talented pilot."
He said Wallis ran a well-organised operation and they were using a brand new machine that was specifically designed to be super safe.
Prime Minister Jacinda Ardern told Newshub she knew how many DoC staff were on-board the flight but would not reveal that information until the victims families were notified.
"DoC staff go out everyday working on our behalf on our environment, sometimes in really dangerous situations and this is an absolute tragedy," she says.
DoC Director General Lou Sanson said he knew all involved in the crash.
He confirmed the chopper was on its way to undertake tahr control in the Haast area when it crashed.
It was a tragedy for DoC staff who were "like family" and passionate about the work they did, said Sanson, who was on his way to the region this afternoon.
DoC's focus was "to support the families and staff as they go through this tough time", he said.
"We are still trying to come to terms with this morning's tragedy. Our hearts go out to the families of the DOC workers involved."
DoC would be liaising closely with the police and would not be commenting further at this stage.
The tahr control operation, which aimed to cull 10,000 of the wild goats over the next eight months, had been put on hold while DoC focused on the tragedy.
In a media statement, the New Zealand Deerstalkers' Association said it "deeply regrets the tragic loss of life" following today's crash.
Former NZDA President Bill O'Leary said the accident and loss of lives was a great tragedy.
"All our members, indeed hunters everywhere, will join in expressing their deepest sympathy to the families of those lost."
Family's flying history
The Wallis family have owned and operated Alpine Helicopters Hanger - now known as Alpine Helicopters and Minaret Station - in Wanaka for 55 years.
Alpine Helicopters' website describes Nick as the youngest of the Wallis brothers. He had 3000 flying hours under his belt and was also a licensed helicopter engineer.
The brothers' father, Sir Tim Wallis, was well-known as a pioneer of the live deer recovery industry in New Zealand and the founder of the Warbirds Over Wanaka airshow.
Sir Tim had survived 15 air crashes with the last one, in 1996 in a World War II-era Spitfire ending his solo flying career and nearly his life.
In 1964, Sir Tim bought his first helicopter and crashed while learning to fly the following year.
The first life-changing crash was in 1968. He was rescuing stock near Queenstown, after a snow storm, and flew his Hiller chopper into power lines.
He injured his spine and wasn't expected to walk again - but did, with the help of a caliper on his left leg.
In 1989, with fuel problems, it crashed in a forced landing at Waipukurau. Another crash followed during a landing in 1992 at Blenheim.
But it was in a different Spitfire in 1996 that Wallis nearly died while taking off at Wanaka. It was a flight in preparation for that year's Warbirds over Wanaka, the hugely popular airshow he had founded in 1988.
Earlier today, Captain Tim Burfoot said the Civil Aviation Authority notified the Transport Accident Investigation Commission of the Hughes 500 helicopter crash accident this morning.
Burfoot told media today a team of four investigators who will start assessing the scene of the crash in the morning.
He said it was not clear what company was involved in the crash, but it was a Hughes 500 aircraft that crashed.
"We believe there was a fire involved when the helicopter crashed."
There are reports that Department of Conservation staff were believed to be onboard the helicopter, which was scheduled to travel to Haast for a cull of tahr (wild goats) on conservation land.
The New Zealand Tahr Foundation (NZTF) - which had opposed the controversial cull along with the NZDA - posted a statement on Facebook extending its sympathies.
"There has been fatalities, and no matter what you think about the tahr issue, these guys were just doing their job," the NZTF posted.
"Our sincere condolences go out to the families of the guys involved - husbands coming home to their families at night is what's the most important here.
"Our condolences also to the team at the Department of Conservation who we have been working closely with over the last few weeks."
Burfoot said he can't confirm how many people were on board but said there were no survivors.
This evening the investigators will liaise with first responders. They will be out at first light to examine the scene, Burfoot said.
There have been "lots" of accidents with Hughes 500 choppers but there was nothing to flag concerns about the craft.
These helicopters are not known to be more dangerous than others, he said.
The Alpine Group general manager of tourism David Hiatt said at 10.51am a helicopter with three people on board left Wanaka Airport for the Landsborough Valley.
The helicopter failed to reach its destination, he said.
Witness: 'There's nothing left of it. Unbelievable'
An eye witness told the Herald that the crashed helicopter has "burnt right out."
"There's nothing left of it. Unbelievable."
He said the helicopter had crashed on DoC land alongside a private property.
McKay said the weather was "perfect" and there was no breeze.
"I'd say it's just a very very unfortunate accident.
"It's a sad day for Wanaka.''
Otago Daily Times reporter Mark Price said he could see the crashed helicopter on a river flat about 100m from the Clutha River and a couple of kilometres from Wanaka Airport.
A police spokeswoman said a member of the public called emergency services shortly before 11am reporting smoke coming from the helicopter.
She did not know how many people were in the helicopter.
Burfoot said it believed the helicopter involved in the crash was a Hughes 500.
"We are in the early stages of gathering information about the aircraft, the circumstances and the people on board," Burfoot said.
"We are working with the emergency services currently on site, who have initial control of the scene."
The Commission was sending a four-person investigation team which was expected to arrive at the site this evening.
The Commission opens an inquiry when it believes the circumstances of an accident or incident have - or are likely to have - significant implications for transport safety, or when the inquiry may allow the Commission to make findings or recommendations to improve transport safety.
Today's crash comes less than three months after Matthew Timothy Wallis was killed in a helicopter crash in the same area.
Wallis was flying alone out of Wanaka, in a Robinson helicopter, on a 15-minute supply trip to lodge in the Minaret Bay area.
A St John spokesman said ambulances and two helicopters were called to the scene, on Kane Rd in Hawea Flats, but had been stood down as they were not needed.
One helicopter landed at the crash scene, but had left.
Flames and smoke were evident prior to the arrival of emergency services, but little of the helicopter itself was visible.
Fire appliances, ambulances and a variety of vehicles from airport and helicopter related businesses were streaming to the scene, though it was apparent nothing could be done for those on board.