According to MANA, The shock writedown is the latest symptom of the dramatic slowdown in the container shipping sector.
Weaker global trade, and in particular softer demand from China, has battered freight rates and left hundreds of ships idle.
"It's really a perfect storm - NYK is a very diversified company with about 30 percent of their revenues coming from the containers business and almost 40 percent from bulk transportation," Ralph Leszczynski, head of research at ship broker Banchero Costa in Singapore.
The shipping industry has been hobbled by losses and debt, with NYK among the most indebted with a $7.2 billion net debt burden at the end of June.
Prior to the warning, shares in the group had closed up 4.6 percent at 206 yen, giving it a market value of $3.4 billion.