Immunisation rates for polio, chicken pox, tetanus and other diseases are significantly down from previous years since the government suspended the sale and distribution of the Dengvaxia vaccine in December, Health Undersecretary Enrique Domingo told reporters.
The government is also investigating Dengvaxia's alleged role in the deaths of at least 14 children who were among the 830,000 who got the vaccine as part of the world's first public dengue immunisation programme in 2016-2017.
The Philippine government is concerned about the potential for epidemics because of lower immunisation rates, he said.
Dengue -- a mosquito-borne disease -- infects 400 million people each year and kills 9,000 globally, the health department said, citing World Health Organisation data.
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The Philippines has one of the highest dengue fatality rates in the world, with 732 deaths last year, it added.
The disclosure sparked nationwide panic, with some parents alleging the vaccine caused the deaths of their children.
"When you go to the communities, all the paediatricians are really heartbroken because all the patients -- the parents (and) the children -- feel that they are going to die," Domingo said.
Sanofi says no one has been proven to have died from the vaccine, but last month the French pharmaceutical giant agreed to reimburse the Philippine government for leftover doses.
"(Three children) died from dengue even though they were given Dengvaxia -- vaccine failure was the possible cause in two of them," the department said in a statement.
Nine others died of reasons unrelated to dengue, while the cause of two other deaths could not be determined.
Asked if the vaccine itself caused the three deaths, Juliet Sio-Aguilar, the head of the inquiry, told reporters on Friday that while it could be possible, "we cannot categorically say."