The memory card problems, which resulted in the machines failing to read the names of candidates off ballot papers, were only discovered during final-phase testing on Monday, one week before the elections.
The introduction of the automated voted system has been controversial, with critics saying many voters do not fully understand the process leaving the door open for electoral fraud.
News of the fault had led to suggestions from some parties and officials close to the outgoing president, Gloria Arroyo, for the commission to delay the vote.
"I would imagine that the success of the automation ... is more important than the timing," Gary Olivar, a spokesman for the Philippine president, said earlier on Wednesday.
"Nobody benefits from a foul up… if technical issues require more time and require us to delay, that is not an unreasonable judgment to make."
Olivar said Arroyo was "concerned" about the technical problems.
"The success of the automated election was one of her beat-the-odds promises at the beginning of her term," he said.
Fifty million voters are eligible to vote in the election to choose a new president and thousands of lower-level officials.
Votes in previous Philippine elections were counted by hand, a process that meant results sometimes took weeks to be announced.
The government decided to introduce a computerised system in an effort to shorten the vote-tallying process to a few days and to minimise the potential for cheating.