A Internet site Mynavi conducted a survay of "popularity vote of font" in 2014. According to it, the most popular font in Japan is MS Gothic.
Here is the ranking of "popularity vote of font".
No. 9 Hiragino
|No. 1||MS Gothic||200||votes|
|No. 2||MS Mincho||166||votes|
|No. 3||HG Maru Gothic M-PRO||54||votes|
|No. 4||HGP Creative Angle Pop||48||votes|
|No. 5||Times New Roman||20||votes|
|No. 8||HGP textbook body||16||votes|
Source is Mynavi.