They will only resume when the pandemic is brought under control.
Authorities in the Mekong Delta province of Kien Giang, home to Phu Quoc, had sought the suspension two days earlier saying the island has limited Covid testing capability and medical facilities and equipment for quarantine, and it could be very dangerous if the infection reaches its shores.
Provincial authorities are seeking to prioritize vaccination for the 100,000 residents of Phu Quoc as the island has got the green light from the Politburo to trial vaccine passports.
Carriers operate 23 flights a week on the HCMC-Phu Quoc route.
The island received over five million visitors in 2019, including 541,600 foreigners.
HCMC is the new epicenter of the current wave and leads the country with the highest numbers of cases, 8,385.
The city is set to make social distancing regulations more stringent from Friday, with residents only permitted to leave home to shop for items like food and medicines or go to work at factories or businesses that are allowed to open.
Earlier the ministry suspended flights between HCMC and Hai Phong and Quang Ninh in northern Vietnam, and Thua Thien-Hue, Quang Nam, Quang Binh, and Gia Lai provinces in the central region.