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Claims in independent and single dependent format and in single independent and multiple dependent formats are all acceptable to the Japanese Patent Office.
When filing an application, the cost is not affected by the number of claims. There is no surcharge for multiple dependent claims. However, when filing a request for examination, the official fee is calculated based on the number of claims.
More information regarding the official fees:
http://www.jpo.go.jp/tetuzuki_e/ryoukin_e/ryokine.htm
See "Schedule of Fees"