Given that Japan's potential GDP growth rate is only around 0.5%, the fact that its economy often falls into negative growth territory should not be shocking:
http://www.telegraph.co.uk/finance/economics/11997884/Japan-returns-to-recession-but-hopeful-signs-suggest-recovery-is-on-its-way.html
There are, however, long-term structural challenges facing the Japanese economy:
http://www.economist.com/news/finance-and-economics/21677648-despite-shinzo-abes-best-efforts-japans-economic-future-will-be-leap