A government audit said last week that almost £91 million allocated over a three-year period had been given to dubious aid groups and ghost projects identified by MPs as beneficiaries.
The scandal centred on a businesswoman alleged to have collaborated with MPs in hijacking some of the funds.
She went into hiding after she was charged with illegal detention of a whistleblower.
Pressure groups say the system promotes corruption and are calling for a protest on Monday to demand that President Aquino abolish the practice.
But Mr Aquino said there was nothing "intrinsically wrong" with the system. Under his new system legislators could still identify projects for funding.
They would however, need approval and would be closely scrutinised, including the publication of bids and awarding of projects.