More than 830,000 Filipino schoolchildren were injected with Sanofi's Dengvaxia vaccine last year in the world's first public dengue immunisation programme.
But the country stopped the sale and distribution of Dengvaxia last month after Sanofi warned the vaccine could worsen symptoms for people who had not previously been infected with the virus.
Philippine authorities are also pursuing criminal and public health safety investigations into any links between the drug and the deaths of 14 schoolchildren who died months after being vaccinated.
Duque also said he had asked Sanofi to refund around 1.5 billion pesos ($30 million) worth of unused vaccines.
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Officials at the government's Public Attorney's Office (PAO), which has been conducting autopsies on some of the dead children, have been trying to build a criminal case by proving the deaths were linked to the vaccine.
The health department has also commissioned independent experts to pursue a separate inquiry in the interest of public health and safety, though the results of this study have not been disclosed.
Sanofi said in a statement on Thursday that it was "saddened" to learn of the deaths of the children.
"Up to this date, there has been no death established to have been causally linked to the dengue vaccine, not even among the 40,000 people involved in the clinical trials conducted across 15 countries," the statement added.
In November last year, the French company released findings of a new study that showed Dengvaxia could lead to severe infections for vaccinated people who caught dengue for the first time.
Dengue, a mosquito-borne illness, is a leading cause of serious illness and death among children in some Asian and Latin American countries, according to the World Health Organization.