Ministry of Health, Labour and Welfare issued the result of their survey National Livelihood Survey 2013 on July 15th. According to it, the average yearly income of Japanese households was 5,372,000 yen ($53,000 €40,000) in 2012. The median income was 4,320,000 ($42,000 €31,500). 60.8% of people live by below the average income.
In the survey, "income" includes taxes and social security charges. So the after-tax pay (take-home money) is less than "income".
The below shows the percentage distribution of yearly household incomes. The next year's version is Distribution of Yearly Household Incomes in Japan, 2013
Figure: Distribution of Yearly Household Income in Japan, 2012
Source is Ministry of Health, Labour and Welfare.