NSO administrator Carmelita Ericta said a majority of the five million unregistered children are Muslims and indigenous people who live in remote areas, far from the nearest town where a childbirth should be reported.
The NSO estimated that three out of 10 children below five years old do not have birth certificates.
Ericta stressed that every Filipino should be registered to include them in basic government programs.
"Filipinos not registered with the NSO can be denied of their rights to go to school, receive health care, obtain a passport, prove their nationality, secure a driver’s license, inherit money or property, own a house or land, open bank accounts, vote or stand for elected office and take (board or bar) examinations," she said.
In an effort to minimize the number of unregistered childbirths, the NSO made an arrangement with the National Commission on Indigenous People (NCIP) and non-government organizations, which included Plan International Philippines (PIP), an international humanitarian organization focusing on the needs of children.
The agreement, dubbed as the Unregistered Children Project (UCP), will be initially implemented in 34 municipalities in far-flung provinces.
The PIP stated national planning for children is "compromised and weakened" if there is no proper registration and accounting of all births in the country.
"Without proper birth registration, a child does not officially exist and is technically a non-living person," the PIP said.
Records showed that in the year 2000, an estimated 41 percent or about 50 million births worldwide were not registered. Two-thirds of the world’s unregistered children came from Asia.