The ministry reported over 797,000 episodes of non-pneumonic acute respiratory infections in toddlers during the period, along with 9,286 cases of pneumonia.
The total number of reported deaths from pneumonia stood at 94 from January 1 to April 28, health authorities said in a bulletin. Most of the deaths were in the southern and southeastern departments — the poorest in the country.
Temperatures there reached 10 degrees below zero Celsius (14 degrees Fahrenheit) in areas with elevations above 3,500 meters (11,480 feet).
Last year, cold temperatures in the Andes killed 359 children under the age of five, according to the Health Ministry.
The World Health Organization says pneumonia is the leading cause of infant mortality worldwide, killing some 1.4 million children under five each year.