Unofficial tallies from Monday's election show Aquino, scion of a political clan that drove the kleptocratic regime of Ferdinand Marcos from office in 1986, has more than 40 percent of the vote, 15 points ahead of former President Joseph Estrada.
The elections were the first to be held in the Philippines using a new automated voting system, and markets had feared technical problems could derail the vote. But the polls went smoother than expected despite problems in some regions.
The official Commission on Elections (Comelec) said on Thursday it had discovered discrepancies between the vote counts transmitted by some of the new ballot machines and vote tallies printed from the machines' memory cards.
"The data transmitted from the machines were accurate but those printed from the back-up memory cards did not match, causing the discrepancy," spokesman James Jimenez said.
He said discrepancies totalled around 150,000 votes. That means Aquino's runaway victory will not be affected.
Monitors said that overall, the elections were fair.
The Asian Network for Free Election (ANFREL) said voting in remote Muslim communities in the southern Philippines was marred by incidents of violence and fraud, including vote-buying, multiple voting, intimidation and harassment.
"There are glitches, there are some problems which should be rectified, but the election is reasonably acceptable," Nepalese monitor Gopal Siwakoti told a news conference.
"The May 10 elections in the Philippines demonstrated notable progress in ensuring freedom of elections with a reasonably acceptable procedure, yet significant room for attaining international commitments and standards." Two presidential candidates, who between them have less than 100,000 of the more than 30 million votes counted, have refused to concede to Aquino, saying they doubt the accuracy and credibility of the automated results.
"We are getting the results fast, but fast does not mean accurate," said Nicanor Perlas. "It is premature to say that the elections were fair and honest." John Carlos de los Reyes rescinded an earlier concession to Aquino after getting reports of possible electoral fraud.
The outgoing speaker of the House of Representatives said he had asked the congressional oversight panel to conduct random audits of Monday's vote to detect any fraud, in addition to the election commission's audit of 1.5 percent of voting machines.
Allegations of fraud surfaced after transmission of results from provincial tallies was delayed, and following the discovery of dozens of machines at the residence of a technician in a city east of the capital on Thursday.
The ANFREL observers showed pictures of voters filling in multiple ballots, children handing out campaign materials and ward leaders distributing cash to people who had voted.
ANFREL sent nearly 40 observers from 16 non-government groups from 13 countries to violence-prone provinces across the country, focusing on the troubled southern island of Mindanao.
