I made an R version of the conversion tool for the names of principal subdivision in Japan.
subdivisionjp.zip (Download page at Google Drive)
(Update: 2013-04-16 22:50 JST)
I didn't know of package Nippon, which includes prefectures table and many other useful features.
I wonder if you should have Unicode data in Unicode character codes like "<U+6771><U+4EAC><U+90FD>" instead of "東京都".
If you have original data in Unicode characters like "<U+6771><U+4EAC><U+90FD>", R console outputs text in a readable way, but the original data itself is less human-readable.
If you have original data directly put like "東京都" (I don't know the name of representation), the original data is human-readable, but console outputs garbled text.