0255 GMT May 28, 2018
Health Under-Secretary Enrique Domingo said many parents were refusing to get their children vaccinated for polio, chicken pox and tetanus, according to BBC.
The fears center 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.
The mosquito-borne disease is a leading cause of serious illness and death among children in some Asian and Latin American countries, according to the World Health Organization (WHO).
Domingo warned, "Our programmers are suffering... (People) are scared of all vaccines now."
He added that vaccination rates for some preventable diseases had dropped as much as 60 percent in recent years — significantly lower that the nationwide target of 85 percent.
Domingo expressed concerns about potential epidemics in the Philippines — a nation of about 100 million people, many of whom are impoverished.
What triggered fears about Dengvaxia?
More than 800,000 children were vaccinated across the country in 2016-17. Fourteen of them have died.
Dengvaxia immunizations were halted last year, as the Philippines launched an investigation into what caused the deaths.
Doctors for Public Welfare (DPW) said a clinical review conducted by Philippine General Hospital forensic pathologists had determined that the deaths were not linked to the vaccine, the Philippine Daily Inquirer reported.
What about Sanofi's reaction?
In a statement, the French company said, "The University of the Philippines-Philippine General Hospital expert panel confirmed... that there is currently no evidence directly linking the Dengvaxia vaccine to any of the 14 deaths.
"In Dengvaxia clinical trials conducted over more than a decade and the over one million doses of the vaccine administered, no deaths related to the vaccine have been reported to US.
"Clinical evidence confirms dengue vaccination in the Philippines will provide a net reduction in dengue disease."
Last November, Sanofi announced that its vaccine could worsen the potentially deadly disease in people not previously infected.
"For those not previously infected by dengue virus, however, the analysis found that in the longer term, more cases of severe disease could occur following vaccination upon a subsequent dengue infection," the firm said in a statement.
Sanofi said Dengvaxia has been registered in 19 countries and launched in 11 of them.
In its latest advice on the vaccine, the WHO said that "until a full review has been conducted, WHO recommends vaccination only in individuals with a documented past dengue infection".