Acting Prime Minister Bill English and Science and Innovation Minister Steven Joyce were deeply saddened by the news that Sir Paul Callaghan had died.
Callaghan was 64 and had been fighting a long battle with an aggressive form of bowel cancer.
His death was confirmed today by the Prime Minister's chief science advisor Peter Gluckman.
"New Zealand has suffered a tremendous loss with the passing of Sir Paul Callaghan. Paul has been our most distinguished public scientist and in the world of molecular physics has been a giant," Gluckman said.
"Sir Paul Callaghan was an outstanding New Zealander who made his mark as a world-leading scientist. He fought a valiant battle with cancer, and has been taken from us far too early," English said.
"Our thoughts are with Sir Paul’s family at this time. His knowledge and willingness to teach others was an inspiration to not only the science community, but New Zealand as a whole. He brought a unique combination of brilliance, integrity and courage to public debate.
"Sir Paul was a true public intellectual who earned the respect of everyone, including those who disagreed with him."
Labour leader David Shearer said Callaghan had a "brilliant mind".
"He was not only one of New Zealand's leading scientists, he was a pioneer. His cutting-edge research in the development of nuclear magnetic resonance methods has had an enormous impact in the areas of medicine, physics and biology.
Shearer said Callaghan was a great man and a gentleman "in every sense of the word".
Prime Minister John Key was probably unaware of Callaghan's death as he was on a flight to South Korea, his press secretary Kevin Taylor said.
It was unlikely that Key would find out about his death until he arrived in Seoul at about 2am tomorrow.
Victoria University Chancellor Ian McKinnon described Callaghan as one of the outstanding scholars of his era.
"With his passing the University has lost an outstanding scholar and researcher. he was somebody who was able to think outside his own scientific disciplines and made a wider community contribution.
"He will be sadly missed by all of us at Victoria University," McKinnon said.
Vice-Chancellor Professor Pat Walsh said though his treatment for cancer was "an immensely difficult time", he went about his work with "characteristic good humour and stoicism".
"He will be dearly missed by friends and colleagues at Victoria, the MacDiarmid Institute and further afield."
Walsh said the university would continue Callaghan's work.
"Paul was the driving force in developing Victoria as a world-leader in this field. His colleagues and students will continue the research that was his passion."
Wellington Mayor Celia Wade-Brown, described Sir Paul as a brilliant scientist and a "very passionate Wellingtonian".
"He really cared about people. He was a very talented and warm-hearted man. We shall miss him greatly. He was very concerned about biodiversity It is a very sad day," Ms Wade-Brown said.
A colleague at Victoria, Assistant Vice-Chancellor Pasifika, Luamanuvao Winnie Laban, described him as inspirational.
"In February Sir Paul and I delivered the Waitangi Rua Rautau Lectures. Paul's speech, laying out his vision for the future of Aotearoa New Zealand, was full of hope, humility, and courage.
"Hopeful, because he was deeply committed to science, education and young people. Humble, because Paul was an ordinary New Zealander who had achieved extraordinary things. Courageous, because he knew his own days were numbered.
"In Samoa, when great people pass we say "Amuia le masina e alu ma toe sau." Envy the moon it comes and goes," Laban said.
The university had set up a tribute page for people to leave messages.
Former students, people who had brief encounters with the scientist, and others who didn't know him personally, but were touched by his work and his death, have already posted messages.
"Paul was to NZ science, what Edmund Hillary was to NZ adventure," one person wrote.
"We need more "Sir Pauls", strong, determined people gutsy enough to promote a different kind of model and create a place 'where talent wants to live'," another person posted.
A WORLD LEADER
After completing his physics degree at Victoria University in the early 1970s, Callanghan embarked on a science career spanning nearly 40 years.
He was knighted in 2009, and received honours almost too numerous to mention through his career, including several prestigious European awards, academic recognition from both Oxford and Cambridge Universities, the Rutherford Medal, a fellowship to the Royal Society of London, a Prime Minister’s Science Prize, and the New Zealander of the Year award in 2011.
He received the Blake Medal from the Sir Peter Blake Trust in 2007.
The trust acknowledged his death on Twitter.
"SPBT staff, alumni and Board would like to pay tribute to Blake Medalist Sir Paul Callaghan. A brilliant man, and a truly sad day for NZ."
The Green Party expressed sadness at the news of the death.
"Sir Paul was a great scientist and public intellectual," said Green Party Co-leader Dr Russel Norman.
"Our condolences and thoughts are with his family and friends at this sad time.
"Sir Paul's contribution to New Zealand extended well beyond his scientific research. He was a fantastic communicator who made science understandable and relevant.
"It is rare to have one person be a leader in so many pursuits. His public service was exemplary.
"Sir Paul had important ideas on the future of the New Zealand economy, in particular how we could seize the opportunities of a modern high tech economy.
"Sir Paul's passing leaves a major gap in our public and intellectual life. He will be missed."
The New Zealander of the Year in February award acknowledged he was battling an aggressive cancer but remained committed to science and had a vision for New Zealand to become "the most beautiful, stimulating and exciting place to live and work in the world".
Callaghan was a world-leading specialist in nanotechnology and magnetic resonance.
He believed that, by attaining economic diversification, New Zealand could reverse the brain drain and make it the place young people chose to build their careers and raise their families while preserving the natural environment and enriching our communities and culture.
He was told in 2010 he wouldn't make it to the end of the year due to the "metastatic stage four cancer".
"Then I had this radical surgery in Sydney in 2010, which was provided by the New Zealand health system."
In January, Callaghan ended his experimental intravenous vitamin-C treatment for cancer, saying there is "absolutely no evidence" it worked. He said he wanted to warn others about the "unusual experiment".
He began receiving the high-dose intravenous infusions in June, along with several alternative herbal remedies.
The scientist began the treatment during a six-month break from chemotherapy, tracking its effectiveness through a blood test for protein carcinoembryonic antigen (CEA), which indicates cancer level.
TRIBUTES POURING IN
The tributes continued to pour in for Sir Paul last night.
The MacDiarmid Institute Board released a combined statement saying Sir Paul was the inspiration and founding Director of the Institute, which carries out research into advanced materials and nanotechnology.
He was also a member of its Board and Chair of its International Advisory Panel. But he was much more than that.
"He was a man of passionate interests and boundless energy. He found time for a personal interest and friendship with all those he worked with, from students he supervised, to colleagues he debated with, and to friends he inspired and loved," the board members stated.
Wellington Mayor Celia Wade-Brown elaborated on her earlier tribute.
"Sir Paul was a great New Zealander and a great Wellingtonian. He was a hugely talented and accomplished scientist and much more besides.
"Sir Paul generously gave of his time and advice to many community initiatives - as an example we were honoured with his presence on the Karori Sanctuary Trust Board - an indication of his passionate interest in the protection of our biodiversity.
"He was a great thinker, business innovator and communicator. He was caring, energetic and above all an inspiring human being," Ms Wade-Brown said.
Dr Garth Carnaby, President of the Royal Society of New Zealand, said Sir Paul was a truly exceptional scientist whose achievements had been recognised at the highest levels both within New Zealand and internationally.
''Paul was undoubtedly one of New Zealand’s most inspirational scientists. His passion for science shone through in everything he did. We will remember him for the excellence of his own personal research, for his inspirational leadership of other scientists, and his ability to communicate about science to one and all.''
Sir Paul was elected as a Fellow of the Royal Society of New Zealand in 1991, and of the Royal Society of London in 2001.
''The Royal Society of New Zealand has benefited enormously from his talents and energy and particularly through his promotion of science to a wider audience over many years. He will be sorely missed by the science community," Dr Carnaby said.
Ministry of Science and Innovation chief executive Murray Bain said Sir Paul would be sadly missed.
''We have not only lost a great scientist, but a great New Zealander. Sir Paul’s formidable intellect and work ethic saw him recognised as a world authority in his field. He deserved every accolade which came his way and will be remembered as a generous and decent person, as well as an outstanding academic," Bain said.
He believed scientists should not exist in isolation.
“One of his passions was bringing science to the people, and he left no stone unturned in achieving this."
Even as his illness reached critical stages, Sir Paul was still committed to the greater good. He undertook a course of intensive Vitamin C dosages in conjunction with a range of herbal treatments, as a scientific experiment to see whether this approach would make a difference.
Bain said Sir Paul’s approach spoke volumes about the man. ''When his treatment proved to be ineffective, he documented the methods and results so others could learn from his experience. Right to the end, he was trying to advance scientific knowledge and help others.''
Meanwhile Science New Zealand chairman and CEO of AgResearch, Dr Tom Richardson said Sir Paul presented an utterly compelling vision that New Zealand can be the best place in the world in which to live and work.
''He inspired policymakers, business leaders, the public, and so many younger people as well as his fellow scientists," Richardson said.
Watch Sir Paul Callaghan talk about conservation and Zealandia