Al Jazeera's Marga Ortigas, reporting from a polling centre in the capital, said many voters had waited for hours outside before the centre opened at 7am, to choose a new president from nine candidates.
Delays in voting
The authorities had expected voters to each take about 10 minutes to cast their ballots but with around 50,000 candidates vying for nearly 18,000 congressional and local positions, many voters were taking much longer to fill in their ballots, our correspondent said.
Al Jazeera's Omar Khalifa, reporting from Cavite, south of Manila, said he saw a number of voters having to feed their ballot papers into the machines several times.
Despite reports of some cases of battery defects, power failures, printing flaws and memory card malfunctions, however, he saw about 100 votes cast into the machines and all were registered successfully.
Gregorio Larrazabal, the election commissioner, said about 300 out of 76,000 machines had problems but that most already were replaced, adding that the problems were "not as widespread as it's made to appear".
"And what's important is that if a machine breaks down, there is a replacement and there is a back-up procedure," he said.
In past elections, manual counts delayed results for weeks and were prone to fraud. But this year, officials are expecting early tallies hours after polls close despite forecasting turnout of around 80 per cent of the country's 50 million registered voters.
Voters appeared undeterred by reports of scattered violence on Monday.
Troops and gunmen exchanged fire in southern Maguindanao province, where 57 people were massacred in the country's worst election-related attack in November, said army Lieutenant-General Raymundo Ferrer.
There were no casualties in Datu Salibo town but in nearby North Kabuntalan township, two civilians were killed in a clash between armed followers of rival candidates for vice-mayor, Ferrer said.
Even with the more than 30 election-related deaths in the past three months, including three on Sunday, election attacks appeared to be down. In the 2007 vote, 130 deaths linked to elections were recorded.
In La Union province in the north, four voters were lightly wounded when a home-made bomb went off at a school doubling as a polling station, police said.
Despite the blast, the elections went ahead as scheduled.
In another incident in the southern city of Marawi, two bombs went off near school buildings, including one school being used as a voting centre, said local military chief Lieutenant-General Ben Dolorfino, adding that they caused no damage or injuries.