This happens every now and then...
The Ministry of Land, Infrastructure, Transportation and Tourism homepage was defaced a few days ago and replaced with a Chinese flag and in English "Don't forget history"
This is a screenshot to a defacement of the controversial Yasukuni Shrine. (Sorry, i couldn't find one of the one mentioned above..)
For being seen as the symbol of the Japanese militant past, it is the by far the biggest target and has been defaced several times by Chinese and Korean patriotic hackers.
(On a side note, Yasukuni is a very beautiful shrine and has an incredibly nice pond and Japanese garden hidden towards the back. (Check it out if you can!) According to one of my teachers who grew up around the shrine and would frequent there for festivals as a child, his image of Yasukuni is as a peaceful place to fall in love.)