He ordered the ministry to immediately arrange flights to transport Vietnamese workers to South Korea and Japan, the country's largest labor export markets, the Government Office said on Saturday.
Other flights should follow with specific safety plans, he said.
Vietnam suspended all international flights on March 25 to stem the spread of Covid-19.
In July the ministry suggested resuming flights to Guangzhou, Phnom Penh, Seoul, Tokyo, Taiwan and Vientiane at a frequency of one round trip per week. The government then agreed to resume commercial flights to and from China.
But the resurgence of community transmissions of the disease in late July put those plans on hold.
The Vietnam Aviation Business Association earlier this month called on the government to resume flights to countries that have contained the pandemic, and allow foreign tourists entry if they meet pandemic prevention requirements.
Those arriving from abroad on special flights currently undergo a two-week quarantine at free centralized facilities or at hotels by paying themselves, but the PM has decided to require everyone to pay from September 1. The government will continue to cover the cost of treatment for Vietnamese nationals. Foreigners have been paying for their own treatment.
On Sunday no new Covid-19 case was reported in Vietnam, the first such day since the second wave began on July 25. Its tally currently stands at 1,040 with 32 deaths.
The outbreak in Da Nang, Quang Nam, Hai Duong, and other localities is mostly under control, health officials said.