Japanese customs has published information regarding the application in Japan of Article 3.16(3) of the EPA.

This information aims at addressing questions raised by importers in Japan and exporters in the EU about additional explanations requested by Japan Customs from importers submitting a claim for preferential tariff treatment under the EU-Japan EPA.  http://www.customs.go.jp/roo/english/text/eu-3-16e.htm

More details.