The bulk of Japan's agricultural imports in 2004 came from the United States and was worth 1,447,444 million yen. This was followed by the EU with 656,290 million yen and China with 565,044 million yen. But, as Asahi Shimbun points out, Japan also exports food, mainly to Taiwan, the U.S. and Hong Kong. Read more here.
The most popular item seems to be Aomori apples! Actually they were even mentioned in today's budget debate in the Lower House, as an example that Japan no longer should just "protect" its agricultural sector, but increasingly think of ways to promote its high-quality foods abroad.
(Photo from this charming Aomori Prefecture website)