The cases came to light after Susilo Bambang Yudhoyono, the Indonesian president, vowed to use "shock therapy" to break the hold of corruption on the country's bureaucracy ahead of elections next year.
The recent allegations against top government agencies have led to calls for Hendarman Supandji, the attorney general, to resign.
He has denied any involvement in the scandal that has rocked his department after a senior prosecutor, Urip Tri Gunawan, was arrested for allegedly accepting a $660,000 bribe from a businesswoman.
Artalyta Suryani, the woman involved, was caught on camera giving Gunawan a cardboard box containing the cash.
She has since claimed the money was a loan and not a bribe.
|Yudhoyono is pushing to clean up government agencies [GALLO/GETTY]
Two days earlier the attorney-general's department had dropped a $70bn corruption case involving Suryani's employer.
Several senior prosecutors have also been implicated in the allegations backed by taped conversations the commission released during the corruption trial.
Al Jazeera's Step Vaessen said the allegations were a major setback for Yudhoyono's anti-corruption drive and have forced the attorney-general's office to take steps to repair its image.
Bonaventura Nainggolan, a spokesman for the attorney-general's department, said prosecutors will no longer be allowed to meet guests whose cases they are handling.
"We have installed surveillance cameras so we can check if people are coming to meet the relevant prosecutors," he told Al Jazeera, adding that 25 prosecutors who were performing poorly will be replaced.
But for anti-corruption activists the changes do not go far enough.
Emerso Yuntho of Corruption Watch said he wants to see Indonesia's top lawyer be sacked.
"The president has no choice," he told Al Jazeera.
"He has to fire the attorney general because he failed to clean up his institution and he doesn’t seem to be taking any quick action to solve the current crisis."