The money became a source of controversy during Aquino's term from 2010-2016,with critics claiming that he used it to barter for favours from legislators. But,he has always denied any wrongdoing.
The charge, filed last week by a special anti-corruption prosecutor but onlymade public on June 20, alleges that Aquino violated the constitution's separationof powers, AFP reported.
In the indictment, prosecutor Conchita Morales alleged Aquino wrote a seriesof instructions to his budget minister to funnel 72 billion pesos into aspecial initiative in June 2012.
Aquino branded the initiative, the "Disbursement AllocationProgramme", an attempt to speed up public spending in the notoriouslybureaucratic nation in order to boost economic growth.
The scheme redirected money left unspent in agencies' budgets to other partsof the government that needed funding for projects.
The programme began in 2012 but Aquino was forced to halt it two years later,after the Supreme Court ruled it violated a constitutional provision whichgives the legislature sole power to authorise government spending.
The prosecutor dropped the case in 2015, but reversed herself followingan appeal by a group of legislators and anti-corruption campaigners. Ifconvicted, Aquino could face up to two years and four months behind bars.
Former budgetsecretary Florencio Abad was also indicted for the same offence.-VNA