The Church appealed for a solemn and prayerful observation of the "day of the dead" and urged against turning gravesites into picnic spots.
Police set up frisking booths at cemetery gates to confiscate alcoholic beverages, playing cards, portable karaoke machines and weapons as huge crowds, including children and the elderly, endured slow-moving queues.
"It is very important for Filipinos to pay respects to their dead. This is also a chance for a family reunion," 21-year-old government worker Mary Joy Pasigan told AFP at a cemetery north of the capital Manila.
Pasigan carried her five-year-old niece past cramped corridors of tombs to offer sunflowers and orchids to her dead grandparents.
Conchita Pura, 60, brought sandwiches for her two-hour vigil at the tombs of her aunt and uncle.
"We come here to light candles and offer prayers so that their sins may be forgiven," she told AFP.
"Getting here is painful, but I must endure it to observe tradition," she said.
The Catholic Bishops Conference of the Philippines meanwhile said praying for the dead was a "duty" as it appealed to Catholics to "bring back the holy".
Instead of adopting Western Halloween celebrations and dressing up as vampires and monsters, Catholics should consider posing as saints, the CBCP said in a statement.
But at the Manila North Cemetery, the mood was more festive than solemn as popular fast food chains set up carts selling roasted pig, dim sum, noodles, fried chicken, and steamed pork buns.
The annual pilgrimage to the cemeteries also triggers a mass exodus from Manila, when tens of thousands travel to interior provinces where their relatives are buried.
Police have been placed on the highest alert since Thursday to secure cemeteries and transport terminals.
President Benigno Aquino inspected Manila's sea, air, and bus terminals on Friday and ordered authorities to remain vigilant, his spokeswoman, Abigail Valte, told state-run radio DZRB
"(Aquino) will spend the weekend monitoring their updates to ensure the safety of commuters who will visit the graves of their loved ones in the provinces," Valte said. - AFP