"The spread of hand, foot and mouth disease is still in a period of ascendancy," ministry spokesman Deng Haihua told reporters.
"The numbers of reported illnesses will continue to rise, we expect to see the peak between May and July," he said.
Deng said that as of April 7, 50 deaths had been attributed to hand, foot and mouth disease, known as enterovirus, this year, with clinics and hospitals reporting more than 115,000 cases.
Nearly 95 percent of cases involved children under the age of five, he said.
State media said on Tuesday that a total of 31 deaths had been attributed to the disease, but Deng said that figure referred to March alone.
Symptoms of hand, foot and mouth disease include fever and sores. It can be fatal in children because their immune systems are immature.
The disease claimed an unusually high 128 lives in China in the first 11 months of last year.