Minamino opened the scoring in the 13th minute, with the Samurai Blue going into the break five goals to the good.
The second half saw a further nine goals – including four inside 11 minutes – as Yuya Osako completed his hat-trick and Sho Inagaki, Junya Ito and Kyogo Furuhashi each twice got on the scoresheet.
Mongolia, ranked 190th in the world, mustered just 20 per cent possession.
The hosts’ goalkeeper, Enkhtaivangiin Monkh-Erdene, faced a remarkable 25 shots on target as Japan maintained their 100% start to Asia’s qualifying tournament after five games.
Another victory over Myanmar on June 3 will secure first place in Group F and a spot in the third round of Asian qualifying.
The game had been scheduled to take place in Mongolia but was changed because of the coronavirus pandemic. The Asian Football Confederation decided this month to play all remaining Group F matches in Japan.