The ministry has sent a document to warn localities nationwide of the epidemic.
The ministry cited a report from the World Health Organisation saying that since April last year, up to 2,522 people in Congo have contracted the disease, including 1,698 fatalities.
On June 11, one person in Uganda was tested positive to Ebola virus after returning from Congo.
To date, Vietnam has not yet recorded any Ebola cases, but the country also faces the risk of viral infection through people who return from the affected areas.
The ministry urged health departments of cities and provinces to keep a close eye on arrivals, including those from countries struggling with the virus.
According to the ministry, people who are suspected to be infected with the virus or returning to Vietnam from Ebola-ravaged areas have to be isolated for 21 days. Their blood samples need to be sent to the National Institute of Hygiene And Epidemiology or Pasteur Institute in HCM City for tests.
Hospitals are asked to enhance measures to avoid cross-infection.
