The disease shows symptoms of fever and a rash most frequently seen on the palms of the hands, soles of the feet, and inside the mouth.
In Vietnam, the most common strain is Enterovirus 71 (EV-71).
A four-month-old baby died in southern An Giang province Feb 28, just one day after contracting the virus.
The same viral toxicity has been seen in Cambodia, where 54 children recently died within 24 hours of contracting the disease.
Japan, Macau, South Korea and Singapore have also reported high numbers of new patients.
Vietnam expects an estimated 100,000 patients this year, the health official said.
The disease can be transmitted though digestive tracts. There are no vaccines or specific medicines to combat the disease and children under five are most vulnerable to it.
The main preventive measures are following hygienic practices in eating and drinking.
In 2012, the disease affected 151,100 people, of which 45 died, according to Vietnam's official records.