Here is the top 10 list of the causes of death in Japan in 2012. 2014 version is "http://nbakki.hatenablog.com/entry/Causes_of_Death_Japan_2014"
|Rank||Cause||Cause||Number of deaths|
|2||心疾患||Cardiac disease||Heart disease||198622|
|4||脳血管疾患||Cerebrovascular disease||Brain vessel damage||121505|
|5||老衰||Senility||Die of old age||60669|
|8||腎不全||Renal failure||Kidney disease||25061|
|9||慢性閉塞性肺疾患||Chronic obstructive pulmonary disease||Cigarette disease||16371|
|10||肝疾患||Liver disease||Liver disease||15944|
The list above is the total number of men+women. For women, rank 9 and 10 are different from this list. Rank 9 for women is Aortic aneurysm and dissociation, rank 10 is Diabetes.
It used to that top 3 was "cancer, heart disease, and brain vessel damage" for a long time. In 2012 lung disease has risen to the third place.
Source is statistics of "Ministry of Health, Labour and Welfare" http://www.mhlw.go.jp/toukei/saikin/hw/jinkou/geppo/nengai12/dl/gaikyou24.pdf