Certain fresh fruits or vegetables & soil
While vegetation is often restricted no matter where you're living, Japan specifically prohibits fruits, vegetables and plants from certain countries and regions. For those hoping to bring fresh fruits, vegetables, spices and plants to Japan, there's a possibility that they may contain harmful vermin that don’t naturally exist in Japan. In addition, no matter where the produce comes from, if there's soil still attached to it, it's not allowed. Soil is one of the prohibited items.
See the official list of prohibited items made by the Ministry of Agriculture, Forestry and Fisheries of Japan before packing. Fortunately, most of the prohibited fruits and vegetables are items that you can already purchase in Japan, so it's not necessary to sneak them into your suitcase as souvenirs and risk breaking Japanese laws.
Certain types of ham, sausage & bacon
All animal products, including meat, organs, eggs, bone, fat, blood, skin, hair, feathers, horn, hooves, tendon, raw milk, semen, feces and urine, must be subject to animal quarantine upon arrival at a Japanese port, even if the products are refrigerated, frozen, cooked or in vacuum-sealed packaging. The inspection certificate issued by your country must accompany your animal products, even when you give a piece of commercially prepared ham, sausage or bacon to someone as a souvenir. In addition, Japan specifies animal products from certain countries and regions that cannot be imported due to the outbreak risk of animal-borne diseases. See the list of countries and regions published by the Animal Quarantine Service of Japan before packing.
Items made from CITES-listed species
Items made from endangered species, and endangered species themselves listed by the Convention on International Trade in Endangered Species of Wild Fauna and Flora, cannot be brought to Japan (for example: tiger fur). If you're unsure, search the CITES database before packing your bags.
All illegal drugs, such as marijuana, hashish and stimulant drugs, are (needless to say) not allowed to be brought to Japan—even if they are legal in your home country. You'll surely be arrested at any ports in Japan if you're caught with these prohibited items.
Weapons such as guns & explosives
While certain guns are technically legal in Japan, the procedure to obtain one is incredibly arduous. So much so, that most people assume they are illegal. However, bringing guns into Japan is most certainly illegal. No matter your citizenship, or whether it's intentional or accidental, you will be arrested if you bring weapons or explosives, such as guns, bombs, chemical or biological weapons and gunpowder to Japan. Furthermore, bringing bullets, even without guns, is also illegal.
You cannot bring designer knockoffs, including counterfeit clothing, bags and watches to Japan. If you intentionally import a large quantity of these items, you may be arrested, your goods confiscated, or both. Even if you're unaware of the counterfeit status of your product, airport screeners may require you to forfeit the offending item. In some situations, you may need to pay a fine.
Uncensored adult videos or books & child pornography
Uncensored adult media, including video, magazines and comic books, and child pornography cannot be brought to Japan. The official reasoning states bringing immoral materials that may harm Japanese public safety is prohibited. Similar to counterfeit products, listed above, penalties are determined by the severity of your infraction.
Counterfeit money & credit cards
If caught bringing counterfeit money, credit cards or marketable securities into Japan, you will be arrested, regardless of where you're from.
In addition to the above, swords, air guns and plenty of medicines and cosmetics are prohibited without a permit. We highly recommend all travelers to familiarize themselves with the details of restricted articles.