Zenbird Quite short, explanatory articles about topics and issues in Japan.
Japan Daily News - news stories in English from the Mainichi Shimbun. (Unlike the Japan Times and Asahi Shimbun), all English stories are available free.
Japan Today News stories from different newspapers and news organisations
Kyodo News English news stories from a Japanese news agency - includes many stories used in the Japan Times
Nippon.com Includes brief news stories, longer in depth discussion of issues, and analysis of data. Many articles can be read in both English and Japanese.
The Diplomat News stories and discussion/analysis in English about Asia, including an East Asia section with articles about Japan
East Asia Forum Articles discussing and anlysing issues, with a section on Japan
The Asia Pacific Journal Longer, mostly quite academic articles, mainly about human rights issues in Japan and East Asia and relations between East Asian countries