"The temperature is increasing leading to more diseases.
"There's going to be propensity for more cholera, dengue, typhoid and malaria," he warned.
Duque added that the diseases are all "manageable" as long as people practise proper hygiene and sanitation and those afflicted are swiftly brought to hospitals for immediate treatment.
The Philippine Red Cross meanwhile confirmed Thursday that three people had died and 2,235 others had been treated in three towns in the southern province of Misamis Oriental for an outbreak of gastroenteritis.
The Philippine Health Department had earlier said the outbreak was believed to be cholera but the Red Cross said tests showed it was gastroenteritis.
Both illnesses have similar symptoms and are spread through contaminated drinking water.
Doctor Eric Tayag, head of the government's National Epidemiology Centre, also confirmed that a typhoid outbreak had hit Real town, northeast of Manila, affecting 109 people. However there have been no deaths from typhoid so far.