The e-visa will not be available for individual applicants.
It is being done through travel companies that are approved to organize package tours, the embassy said on its website.
On arriving at airports, visa applicants need to present the "Visa issuance notice" displayed on their mobile phones.
Vietnam has been one of Japan's seven biggest tourist sources this year with 397,000 arrivals, according to the Japan National Tourism Organization.
In 2019, the year before the onset of the Covid, 500,000 Vietnamese tourists visited Japan.
Japan is one of 13 countries for which Vietnam has unilaterally waived visas.
