Health Under-Secretary Enrique Domingo said many parents were refusing to get their children vaccinated for polio, chicken pox and tetanus.
The fears centre on Dengvaxia, a drug developed by French company Sanofi.
Sanofi and local experts say there is no evidence linking the deaths of 14 children to the drug.
However, the company had warned last year that the vaccine could make the disease worse in some people not infected before.
Dengue fever affects more than 400 million people each year around the world. Dengvaxia is the world's first vaccine against dengue.
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