January – Diplomatic relations between Palau and the Philippines reach an all-time low with Palau President Kuniwo Nakamura threatening to sever diplomatic ties between his country and the Philippines over repeated crossing of Filipino fishers into Palau's EEZ.[1][2]
January 6 – A giant wave hits the wharf of Sitangkai, Tawi-Tawi, causing damages to properties and reported deaths of 18 people.[3]
January 19 – During a fluvial procession in Lumban, Laguna, a float hits an electric cable which later falls, causing devotees aboard to get either electrocuted or drowned as they jump into the river; 13 are confirmed dead, others are reported missing.[4][5]
March 14 – Electorates of the municipality of Ilagan, in the province of Isabela turn down the cityhood law under the Republic Act 8474 which seeks to convert the town into a component city.[11]
June 22 – Mayon Volcano in Albay suddenly and shortly erupts, emitting ash as high as 7 to 10 kilometers; ashfalls are reported in Camalig; there are no casualties.[13]
Mid-August to early September – Sixty-eight residents mysteriously died in Clark, Pampanga. In October, a task force reported that the deaths were caused by tons of toxic waste abandoned in the former US air base.[20]
September 16 – The Supreme Court grants a petition declaring Republic Act 8528 unconstitutional which amended certain sections of Republic Act 7720, citing lack of plebiscite. Thus, the component city of Santiago in the province of Isabela is reverted to an independent component city.[23][a]
October
October 23 – A plebiscite creating the city of Novaliches is held but the proposal is turned down by the electorate.[25]
October 31 – An overloaded jeepney plunges into the ravine in Itogon, Benguet, killing 21 passengers out of 34 people on board.[26]
November 18 – At least 32 die in separate clashes between MILF rebels and government troops in the provinces of Lanao del Sur and Maguindanao, a day after their declaration of a ceasefire.[28]
December 15 – The Metro Rail Transit Line 3 (MRT 3) is opened to the public with operations running along a 16.9-kilometer route from North Avenue in Quezon City to Taft Avenue in Pasay City.
As per Executive Order No. 292, chapter 7 section 26, the following are regular holidays and special days, approved on July 25, 1987.[35] Note that in the list, holidays in bold are "regular holidays" and those in italics are "nationwide special days".
January 21 – Dr J Ana Water Dispenser captured the 1999 2nd Yakult PBL Centennial Cup crown, becoming the 1st title to win the tournament, defeating Tanduay Gold Rhum Masters, three games to two.
July 1 – The Welcoat House Paints were crowned the 1999 Yakult-PBL Challenge Cup champions after clinching an 80–74 victory over the Red Bull energy Drink in a Game 4 for the title at the Makati Coliseum
December 8 – The Manila Metrostars rout the Cebu Gems, 101–83 in Game Six, before a hometown crowd at the Mail & More Sports Complex in San Andres and crowned themselves the 1999 MBA national champions.
December 12 – The San Miguel Beermen captured their second straight title of the season with a 4–2 series victory over Alaska Milkmen. The Beermen won their 13th PBA crown and are now the winningest ballclub, tied with the famed Crispa Redmanizers for most titles.
^Event occurred Sept. 16 based on court records. At least another source states the date as late as Dec. 29; however, this information conflicts with the former.[24]