The bilateral EPA with Japan and Vietnam ("JVEPA") was entry into force on October 01, 2009.
According to the web site of Ministry of Economy, Trade and Industry ("METI") of Japan on November 05, the practical operational procedure regarding JVEPA was notified by Vietnam government as follows. This information is largely for Certificate of Origin ("CO") in importing the goods into Vietnam.
1) In case the CO of JVEPA is not available on hand in declaring import into Vietnam, according to MOF Notification No. 45 (on May 07, 2007), the importer should pay the customs duty of MFN rate with notifying to Customs on document that the CO will be submitted later.
Then, within 30 days, by the importer submitting CO (Form VJ) to Customs, the duty amount difference between MFN and EPA preferential tariff shall be reimbursed.
2) Even if the further late submission of CO more than 30 days since import declaration, the importer still can be reimbursed the duty amount as long as the CO is valid (One year since issuing date). However, please be noted such late submission is subject to administration penalty of late submission based on MOF Notification No. 45 (on May 07, 2007).
3) The goods exported from Japan before October 01, 2009 can also be treated same manner as above 1) and 2) regardless of the arriving date of Vietnam.
(Source: http://www.meti.go.jp/policy/trade_policy/epa/html2/091105JVEPA_kanzeikanpu_oshirase.pdf )