Katsuhiro Noguchi beat nearly 90,000 entries from 21,000 amateur and professional photographers worldwide to win a prize worth 1.5m yen (around £8,000).
Around 150,000 people were reportedly evacuated after the nuclear incident at Fukushima following the earthquake and tsunami on 11 March 2011.
Katsuhiro uses a Canon EOS-1Ds Mark II and began taking photos of Fukushima’s flowers four years ago.
Katsuhiro said: ‘Whenever I am behind the lens, two hopes occupy the corner of my mind: to brighten the city and to encourage the people with flowers.
‘The Great East Japan Earthquake and subsequent nuclear accidents significantly impacted our quiet life, and as a resident of Fukushima, my future was also heavily shrouded in uncertainty.
‘And yet, even in that situation, the plants in the fields sprouted the same as ever, carrying our hopes with them.
‘Even in that chaotic spring, where the earth was damaged, the scene of those buds sprouting as always, without losing their way, filled me with a sense of deep compassion and serene strength that I cannot describe in words.
‘Since then, photographing and presenting the “Flowers of Fukushima” has become my lifework.’
Thyago Nogueira, one of the judges, said: ‘By avoiding overly seen images from the tragedy, the series expands our visual representation of a disaster.’
Fellow judge Sophie Stafford added: ‘In this winning image, a powerful and moving story is expressed through an artist’s eye.
‘The flowers are a vibrant and captivating promise of better things to come.
‘Despite their fragility they have conquered tragedy. As a photo, it is technically excellent. As a testimony to hope, it is unparalleled.’
Katsuhiro added: ‘In the beginning, I immersed myself in taking pictures of flowers to avoid the harsh reality left by the earthquake.
‘However, at some point I began to feel peaceful when photographing flowers.
‘Gradually, I developed bonds with my neighbors, who offer me flowers, and now I am experiencing a true wonder, an everyday joy that comes to everyone who centers their life around flowers.’
The Nikon Photo Contest awards ceremony is due to take place in Shanghai, China on 14 July.
The first Nikon Photo Contest was held in 1969.