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We like to distribute FCC conforming products in Japanese market by affixing the VCCI mark on them. What shall we do?

FCC conformity does not have effect in the Japanese market. Please file conformity verification report to VCCI in accordance with the VCCI rules.

I understand that there is MOU established between Japan and the US. Under the circumstances will VCCI accept FCC test report as VCCI conformity verification report?

You cannot have VCCI conformity verification report substituted only by FCC test report. You need to do the testing based on the VCCI Technical Requirements of the current year version (V-3/2015.04 for instance) and record the fact in the test report. Incidentally, VCCI conformity verification test shall be performed in the test facilities registered to VCCI.

We have a plan on marketing a certain product in Japan, North America, Europe and Asia. Will we have to go through EMI regulatory process in all regions independently? Either that or one filing in a region or country will do the job once for all?

EMI is regulated country by country in the law or its substitutes. The VCCI rules are good only in Japan. Each country or region has its own standard, FCC for the US, EN for Europe and National standard for each country in Asia. They either check the conformity by testing or accept self declarations.