But a spokesman for Arroyo - who has promised a smooth transition before her term ends on June 30 - said on Wednesday that the outgoing president was ready to face an investigation and would not enjoy any legal immunity.
"This offers the president an opportunity to answer these accusations, to clear the air and submit herself to the judgement of history," Gary Olivar, the spokesman, told the AFP news agency.
Aquino, who was once taught economics by Arroyo, said she should be investigated over a phone call she allegedly made to an election commissioner during the last election in 2004.
Arroyo is suspected of being the voice in a telephone recording of a woman appearing to press an election official into ensuring the 2004 vote count stayed in her favour.
Arroyo has apologised for making the call but denied any wrongdoing, and has ridden out past impeachment attempts in congress with the help of legislators allied to her.
Aquino, who campaigned on pledges to investigate allegations of electoral fraud, corruption and rights abuses by the outgoing administration, said there was a "necessity also for reforming our judicial system so we are not locked in a battle in the courts in the next two decades".
"We need to have closure on all items like the fertiliser scam. We lost 720 million pesos ($16m). Who is responsible for this? Let's also look at the ZTE."
In both cases Aquino mentioned, there are allegations of overpaying for deals and diversion of funds.
"There is no reason why you cannot expedite the solution of these cases," Aquino said.
"I still have to consult the DOJ [justice department] on how best to go after this."
With nearly 80 per cent of ballots counted from Monday's polls, election commission Comelec has stopped updating its unofficial tallies, having said Aquino had more than 40 per cent of the votes, far ahead of former president Joseph Estrada's 25 per cent.
Arroyo's chosen successor and former defence secretary, Gilberto Teodoro, was running a distant third.
But a winner can only be declared after all the results are in and Estrada has said he will not concede based on unofficial results, though he does not plan any protest of the outcome.
The US and EU hailed the overall conduct of the vote, despite scattered outbreaks of deadly violence and some problems with the automated ballot-counting machines.