No vaccination certificates are required for entry to Japan, but a vaccination for influenza is sometimes recommended for travel between November and April. Long-term travellers, staying for more than a month in rural areas, should get a Japanese encephalitis vaccination if they are travelling between the months of June and September. There have been recent outbreaks of the deadly bird flu in Japan, but no human infections have been reported and travellers are unlikely to be affected; as a precaution, live animal markets and places where contact with live poultry is possible should be avoided, and all poultry and egg dishes should be well cooked.

Medical facilities are very good in Japan, but medical assistance can be very expensive and visitors have to pay the whole cost up front. Travellers should ensure that they have adequate medical insurance before travelling. The possession of Vicks inhalers and other common medications used for allergies and sinus problems are banned under the strictly enforced anti-stimulant drugs law, and visitors are advised to check with the Japanese embassy if in doubt. It is always best to take prescribed medications with you when you travel, in the original packaging and with a signed and dated letter from your doctor detailing what the medication is and why you need it.