The move was based on proposals from the northern province of Quang Ninh and the Central Highlands province of Gia Lai as a measure to reduce risk of the disease spreading until the situation in HCMC was brought under control.
Quang Ninh is home to the UNESCO heritage site Ha Long Bay while Gia Lai is a lesser-known tourist destination famous for tea estates and rubber plantations.
On Thursday, the ministry had suspended flights between Hai Phong City and HCMC for the same reason.
Aviation authorities have already limited domestic flights to and from HCMC’s Tan Son Nhat Airport for two weeks starting Tuesday.
HCMC has been grappling with a surge in community transmissions over the past week, mainly linked to a cluster at Christian congregation Revival Ekklesia Mission.
The city of 13 million began two weeks of social distancing last Monday. It has so far recorded 355 infections in the fourth wave that hit Vietnam starting April 27.