Sir Paul Callaghan, 63, a professor of physical sciences at Victoria University in Wellington, founded technology company Magritek.
He is widely published -- over 240 scientific papers and one book -- and in 2009 was knighted for his work.
Last year he won the Prime Minister's Science Prize and the Gunther Laukien Prize for Magnetic Resonance.
Awards patron Jim Bolger said Sir Paul had shown outstanding leadership as a scientist, teacher and communicator.
"Sir Paul has done so much to raise the profile of New Zealand as a leader in the field of science," he said.
"His commitment in connecting science, technology and business for the positive economic development of New Zealand is inspirational and encourages others to also make a difference."
Accepting his Kiwibank-sponsored award at a ceremony in Auckland tonight, Sir Paul said he had been fortunate to work in a field he loved.
"I am humbled and honoured to receive this award, especially when there are thousands of people who are making enormous contributions to New Zealand every day," he said.
"My hope is to make science and innovation a core part of our country's future and to encourage more talented young New Zealanders to take every opportunity they can."
Also shortlisted for the prize were sustainable business leader and philanthropist Peri Drysdale and founder of Male Youth New Direction, a programme for serious youth offenders in South Auckland, Stephen Boxer.
Each winner received a handcrafted trophy and $5000.
Four other people were also honoured at the event:
* Alison Neill, 78, from Fairlie, in South Canterbury, was named Countdown Senior New Zealander of the Year for over 30 years of volunteer carer to the elderly.
* Jamie Fenton, 17, from New Plymouth, was named Coca-Cola Amatil Young New Zealander of the Year for her work as a young inventor and inspirational role model.
* Billy Graham from Naenae, in Lower Hutt, was given the Kiwibank Local Heroes Award for his work creating programmes for at-risk youth.
* The Gibbston Community Association, in Central Otago, was named Mitre 10 Community of the Year for its outstanding community development achievements.
