The EACC and Treasury will undertake an IFMIS audit from December to find loopholes used to steal billions of shillings in taxpayers’ money.
Commission deputy CEO Michael Mubea said on Friday that abandoning the system will not solve corruption in government institutions.
“We will be undertaking a systems review to identify the weaknesses and loopholes that exist and (make recommendations on how to seal them,” said Mubea.
He spoke at the close of the EACC workshop on corruption in the devolved government, that took place at the Whitesands hotel in Mombasa.
Mubea decried lenient sentences and fines handed to those convicted of corruption, saying they do little to deter corruption.
He gave the exampe of Chinese nationals who pleaded guilty to bribing government officers with Sh30,000, and noted they were fined Sh70,000 and allowed to carry on with their businesses.
Mubea said Kenyans would like to see convicted corruption suspects jailed instead of paying fines and walking free.
He said a lot is being done to fight corruption but that the public only hears about a few aspects, leading to the view that not much action is being taken.
Regarding the alleged theft of Sh51 million from Kilifi county coffers, he noted: "You will see suspects in court in the next two weeks."
But the deputy chief executive said the commission was yet to get an official complaint on the Sh1.8 billion Kilifi county money, said to have been misappropriated.
“We are only hearing and reading about the amount in the media,” he said.
This comes a day after Deputy President William Ruto ordered a probe into the alleged loss of the money.
“So long as a sentence is lawful, it is a sentence. Where the sentence meted out appears to be lenient, one has to investigate the record and the circumstances of the commission of the offence. First offenders are not treated the same ways as repeat offenders," she said.
“But I do agree, for criminal cases we must get firm and give stiffer sentences as the circumstances of a case require. Each cases is to be determined by its own peculiar facts and circumstances."
The DCJ, who was on her first function out of Nairobi since she was appointed, reiterated the Judiciary’s commitment to fighting corruption.
But she said investigators, prosecutors and adjudicators (Judiciary) must play their parts effectively.
Mwilu further said the Judiciary has fast-tracked corruption cases, which are now heard on a daily basis.
A special division of the High Court was set up and dedicated to hearing the cases.
“Once a cases starts, we will not have it adjourned until determination is given,” said Mwilu.