In an urgent document sent to hospitals, the department said that more measures are needed to prevent a possible outbreak of the disease.
It also asked hospitals and clinics to quarantine infected patients.
In addition, the department will also look at staff training, facilities and medical equipment and supplies to ensure that measles is treated correctly.
Patients and family members have been urged to protect themselves and wash their hands regularly.
Last December, health officials in Hanoi raised concerns over a possible outbreak of a new measles epidemic because nearly 33,000 children had not been vaccinated.