Hundreds of anti-riot police were stationed outside the palace of Susilo Bambang Yudhoyono, the president, before the rallies went ahead.
Yudhoyono on Monday told The Jakarta Post that he believed the protests were partly aimed at destabilising his government.
"My logic says these political movements want to discredit, shake and topple me in the short term,'' the newspaper quoted him as saying.
Yudhoyono faces questions over the last year's 6.76 trillion rupiah ($715m) government bailout of a bank, which critics have alleged was full of irregularities.
Indonesian politicians last week launched an inquiry into allegations that the bailout benefited Yudhoyono's re-election campaign - a claim he denied.
The government's commitment to end corruption was also hurt when investigators concluded that senior police tried to frame anti-graft officials from the Corruption Eradication Commission on made-up charges of bribery and blackmail.
Yudhoyono was re-elected in July on promises of stamping out corruption.