Voting time was extended by 1 hour because of system delays and long lines.
The BBC reported as many as 85 percent of the 55 million eligible voters were expected to cast their ballots.
Nine candidates vied for president. Citizens also voted to pick thousands of national and local leaders. Amnesty International had said pre-election violence claimed a number of lives, and condemned the use of private armies by candidates.
The front-runners in the presidential contest were Sen. Benigno Aquino III and former President Joseph Estrada, CNN reported. Aquino, is the son of the late Sen. Benigno S. Aquino Jr. and former president Corazon Aquino.
Despite the voting delays, The New York Times reported results were still expected to be announced in the next two days.
Kontra Daya, an election watchdog, reported counting machines broke down in nearly a dozen precincts in the capital, the report said. There were also complaints of voter lists missing and vote-buying.
In the violence-plagued southern region of Mindanao, there were reports of more violence and disorderly conduct, the report said.
Gunbattles and bombings were reported in the region's Maguindanao area, which became notorious late last year when 57 people were massacred in the country's worst incident of political violence.
The Times report said voting was suspended in the southern town of Kabuntalan following the deaths of two people in gunbattles.
A day prior to the election, five people died in separate election-related incidents.
Besides the presidential vote, candidates were contesting for some 18,000 local, regional and national posts, the Times said.