According to Article 3(1)(v) of the Japanese Trademark Law,

Any trademark solely consisted of a very simple and common mark may not be registered.

 Trademark Examination Guideline(TEG) pertinent to the article (Chapter I, Part 7) specifies that:

Trademarks composed of (a) one or two alphabetical letter, (b) two alphabetical letters hyphened, or (c) one or two alphabetical letter preceded or followed by a term representing business entity, e.g. “Co.” “Ltd.”, are not registrable on the grounds of Article 3(1)(v).

 In the meantime, trademarks consisted of (a) two alphabetical letters combined with “&”, (b) two alphabetical letters depicted in monogram, (c) Japanese katakana characters transliterating two alphabetical letters, or (d) two alphabetical letter represented in a unique design do not fall under the article.

 http://www.jpo.go.jp/tetuzuki_e/t_tokkyo_e/pdf/tt1302-002/1-7.pdf

You had better note that TEG admits to register Japanese katakana characters transliterating two alphabetical letters. That means, even if alphabetical letter trademark would fail to register due to the article, you may have an option to register transliteration of the mark in Japan.

Consequently, one or two alphabetical letter trademarks in standard character, including acronyms and abbreviations are under normal circumstances not registrable.

 As an exception, provided that the producer so effectively markets the product with the mark that consumers come to immediately associate the mark with only that producer of that particular kind of goods and thus one or two alphabetical letter trademarks attain acquired distinctiveness, the marks are entitled to trademark protection on the basis of Article 3(2).

 

Article 3(2) of the Japanese Trademark Law stipulates that:

Notwithstanding the preceding paragraph, a trademark that falls under any of items (iii) to (v) of the preceding paragraph may be registered if, as a result of the use of the trademark, consumers are able to recognize the goods or services as those pertaining to a business of a particular person.