According to
http://togetter.com/li/399927 , quite a few manga publishers like shougakukan and houbunsha once issued guides that effectively mean all secondary creation (doujin) are prohibited. People analyzed that it is a "better safe than sorry" strategy that whenever anything happen like if some other company want to sell things base on their own series, then the publisher can take these guidelines out. But these guidelines could become a problem with TPP.