Its Foreign Ministry said the 36 have been moved from a Level 2 warning, under which citizens are required to refrain from all non-essential travel, to Level 1, the lowest in its four-point scale, Japan Times reported.
The ministry said globally there is a downward trend in the number of new Covid-19 infections and deaths, and the risk of severe symptoms and deaths is receding.
Nevertheless, it advised Japanese citizens to "stay fully alert" even when visiting Level 1 countries.
Vietnam had over 9,300 new cases last week, down 24 percent from the previous week.
Vietnam has allowed quarantine-free entry since March 15 and recently waived the requirement for Covid tests.
Japan has also scrapped mandatory quarantine for people arriving from Vietnam if they have got three vaccine shots.