Nearly 87,000 candidates are running for political posts in the elections, with virtually every elected post bar half of the 24-seat senate and the positions of president and vice-president contested.
But despite calls for change from several quarters, and Arroyo's own unpopularity, most observers expect little change to the political status quo.
Opinion polls show the opposition is likely to hold onto the senate while Arroyo's allies will retain control over the House of Representatives.
|Across the country nearly 87,000 candidates |
are standing for election [Reuters]
Many of the 45 million registered voters started queuing up early in the morning outside the 300,000 polling centers.
Arroyo herself was one of the first to cast her ballot in the town of Lubao north of Manila.
"The Philippines is at a crossroads as we wait for the proclamation of winners," she said in a statement.
"For the sake of the nation, we should put a closure to all chapters of conflict and battles once the nation makes its decision, and open all doors to national reconciliation and unity."
Arroyo's six years in power have been a mixed bag of steadying the economy while lurching from crisis to crisis, including at least two coup plots, terrorist attacks and a string of natural disasters.
She will be ineligible to seek a re-election after her term ends in 2010.
But critics say Arroyo could renew a failed bid to change the constitution to adopt a parliamentary system in an attempt to extend her tenure.
Across the country election day saw security forces on full alert after more than 116 people were killed and 121 others wounded in violent attacks during the campaign period.
In the latest incident on Monday, a village chief in the northern Abra province was shot dead during a scuffle after he questioned the presence of unidentified armed men.
Other deaths were also reported on the southern island of Basilan, but warnings that communist rebels in the south might try to disrupt the balloting with a rash of attacks proved to be unfounded.
Whilst the current election has scored a bloody tally, the body count is still lower than the previous elections in 2004, which claimed 189 lives.
Al Jazeera's correspondent in Manila, Marga Ortigas, says that with such a high death toll, many voters said casting their vote had been all the more important.
Initial results from the vote could start coming in by Thursday, but with complex ballot papers counted by hand the final tally could take at least three weeks.
Critics of the manual voting and counting system argue it can be easily manipulated by switching ballot boxes and paying off vote counters – usually poorly paid public school teachers - to tweak the figures.