From the Japanese Customs Website, prohibited items do not include any food items directly. You can see for yourself by clicking on the linked words.

You can also find all the import and export mailing procedures here:
http://www.customs.go.jp/english/c-answer_e/customsanswer_e.htm#kinsei

Then I went on to look at the items in the restricted section, and it said this:

--------Quote:
# Rice, flower seeds/bulbs, flour, straw and straw items
# Fresh fruit, meat products and vegetables (pineapples, green bananas excluded)
# Items requiring Quarantine Certificate are rooted plants, furs, straw products, shells, meats and stuffed animals
# Wildlife products from protected and endangered species

----------/Quote

AND

------Quote:
* Three (3) bottles (around 760cc) alcoholic beverages
* 400 pieces of cigarettes per adult
* 100 pieces of cigars (if there is no other tobacco)
* 500 grams pipe tobacco
* If there are more than 2 kinds of tobacco, up to 500 grams in total weight
* 2 ounces perfume
------------/Quote

I can't link to them directly, because they were popups, but the main link above will get you to them.

There is nothing indicated about prepackaged prepared foods.

However, if you want to save yourself the hassle of going through customs yourself and filling in all the forms and paperwork, why not consider ordering from a company that ships to Japan for you, and they take care of the paperwork?

amazon.com has a gourmet foods and a regular foods section on the website with all kinds of choclates and snacks, and they ship to Japan:

http://www.amazon.com/gp/help/customer/display.html?nodeId=596200

That would cut out some of the hassle for you and then you'd know for sure the item can be shipped.

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