Allegations of the corruption center around an economic stimulus package the government issued during the recent global recession. There are accusations that much of the stimulus money lined government official's pockets or their friends at banks.
From CNN World, writer Kathy Quiano gives us more details on the corruption.
The protests come amid a growing public dissatisfaction over investigations into a bailout of Indonesia's Century Bank.
The controversy began when critics accused President Susilo Bambang Yudhoyono and some of his political allies of benefiting from the bailout money. The $710 million government bailout occurred in November 2008.
In the South Sulawesi capital of Makassar, where protests are typically more violent, hundreds of demonstrators called for the resignation of Indonesian Vice President and former Central Bank Governor Boediono and Coordinating Minister for Economic Affairs Sri Mulyani.
Both were blamed for key roles in the bailout.
In Jakarta, protesters chanted: "Down with corruptors" and other slogans. One group burned a picture of Boediono.
"We know that corruption is the source of stupidity, poverty and social imbalance," protester Fadjroel Rachman said. "We are expecting the world to bring down all the corruptors as well as Indonesia. Whoever the corruptor is, we have to take them down. If you're not a corruptor, there is no reason for you to be afraid."