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As of 1 July 2007, when you enter Japan, you are required to submit a Customs Declaration Form for both your accompanied and unaccompanied baggage at the Customs Clearance. These forms are available on the aircraft/ship or at the Customs Office.
For the purpose of preventing acts of terrorism, all foreign visitors wishing to enter Japan are required to have their fingerprints and a facial photograph taken, after which an immigration control officer will conduct an examination for landing.
anyone who refuses these procedures will not be permitted to enter Japan, apart from the following:
1) Special permanent residents
2) Persons under 16years of age
3) Persons performing activities which fall under the status of residence for 'Diplomat' or 'Official'
4) Presons who have been invited by the head of any national administeative organixation
5) Persons who are prescribed by a Ministery of Justice ordinance as equivalent to either 3) or 4)
[More information: http://www.immi-moj.go.jp/english/index.html]