Hundreds of Vietnamese nationals gathered at Narita Airport, east of Tokyo, on Saturday to board "rescue flights" to return to their home country.
The Vietnamese government had operated flights to repatriate people under special circumstances, including those who were ill or pregnant. But the service was suspended in mid-May due to stepped-up entry rules.
About 300 Vietnamese nationals, including trainees and students, boarded two flights that were operating for the first time in about three weeks.
One student said he wanted to return home for a year, and that he is happy that he will finally get to see his girlfriend and parents again.
Many people who were unable to get tickets gathered near the check-in counter, hoping for cancellations.
The Vietnamese embassy says about 7,000 Vietnamese had indicated they wanted to return to Vietnam as of end of last month, but that there are no plans to operate any more rescue flights this month.
Meanwhile, the Japanese government is stepping up entry rules due to the spread of a new variant in Vietnam.
Effective Friday, people entering from the country are required to stay at accommodations secured by the government for the first six days of a two-week quarantine period.