It's a function of their money supply growth - which is now extremely low. Back in the 70's and 80's during the Japanese Bubble, it was relatively much higher.
Prices are a rather fuzzy function of the money supply, total production, and the supply of credit (for things customarily bought with debt). GDP is calculated by adding up prices of goods and services sold. Even though it is typically corrected for inflation growth, this doesn't adequately compensate for monetary growth, because production growth acts to reduce prices, and the two mask each other to some extent.
tldr: GDP is a terrible way to measure a countries output/growth.
Why is Japan's GDP growth looking like this: http://www.tradingeconomics.com/japan/gdp
Not that I don't like posts about management techniques but from Toyota (their best years are also some time ago) from Japan... I don't know.