The Ethics and Anti-Corruption Commission now says that Nairobi, Kilifi, Kajiado and Narok are among counties with the most serious revenue accountability shortfalls.
In a statement detailing how counties have allegedly been embezzling public funds, the Anti-graft body said it is taking necessary legal action as it is mandated.
The Commission noted that while the deployment of integrated revenue management systems in counties is aimed at enhancing efficiency and accountability, the systems are increasingly being manipulated to divert public funds to private individuals.
It said that this is usually done through collusion involving Governors, senior county officials, and companies providing the revenue management service.
"Nairobi, Kilifi, Kajiado, and Narok are among the county governments with serious accountability deficits in their revenue management systems.
"The Commission is taking appropriate action in accordance with its mandate," EACC said on Thursday.
EACC said that some of the looting systems are designed from the time the contracts are awarded. Such contracts, the Commission said are awarded to people linked to county staff.
"In this emerging pattern of automated looting of public funds, contracts for revenue management systems are designed with inbuilt corruption ranging from irregular tender awards favouring entities linked to county officials to fraudulent dealings within the automated systems.
"In some counties, the revenue systems are entirely controlled by private entities while in others, officials run parallel revenue systems."
EACC said that reports also point to senior county officials altering revenue data to divert funds to private bank accounts.
The Anti-graft body is now calling for an audit of the revenue management systems in the county governments.
On Monday, EACC ordered Kilifi County to stop the planned payment of Sh103 million to allow for investigations.
According to EACC, preliminary investigations indicate that the successful bidder, a construction company, allegedly did not have the requisite capacity and experience in undertaking revenue management and collection.
EACC said that the company, in support of its bid, allegedly annexed documents belonging to a third party.
