The National Prosecuting Authority (NPA) and the South African Revenue Service (Sars) are set to come under the microscope as President Cyril Ramaphosa attempts to clean house in 2018.
Speaking in Parliament during his first State of the Nation Address on Friday night, Ramaphosa committed to tackle corruption in the public and private sector.
For this to happen, he said law enforcement agencies and other institutions needed to step in to protect the public purse.
The leadership of both the NPA and Sars, widely seen to be loyal to Ramaphosa's predecessor, Jacob Zuma, have come under fire for not acting against corruption and the looting of state resources.
"We will urgently attend to the leadership issues at the National Prosecuting Authority to ensure that this critical institution is stabilised and able to perform its mandate unhindered," the president said.
Tax revenue was expected to fall short by over R50 billion, increasing pressure on the already strained fiscus.
"We will also take steps to stabilise and strengthen vital institutions like the South African Revenue Service," said Ramaphosa.
"We must understand that tax morality is dependent on an implicit contract between taxpayers and government that state spending provides value for money and is free from corruption."
Ramaphosa said he would appoint a commission of inquiry into tax administration and governance at the request of current finance minister Malusi Gigaba "shortly", something Zuma committed to do last year.
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