EACC has recommended prosecution of seven governors after probe on graft allegations.
The Ethics and Anti-corruption Commission
boss Halakhe Waqo however declined to mention their names during the opening session of four-day workshop on corruption at the counties.
Waqo said in Mombasa that county governments have emerged as the most corrupt institutions of late.
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He said that the commission has directed the Director of Public Prosecution (DPP) to charge the seven governors of which two had taken plea over corruption related cases.
A survey done by EACC between April and June 2015 revealed that corruption is high in the county governments.
Waqo said the survey was aimed at mapping out corruption prone areas and unethical practices in the county governments.
"The five had not appeared in court to plead to the charges since they had obtained orders in court to stop their arrest," he said.
"Graft thrives in procurement, finance, public service board, road and public works departments," he said.
He further added that the specific forms of corruption are evident in procurement irregularities, conflict of interest in awarding tenders, bribery and political influence in tendering.
Waqo said corruption remains an impediment to county development; inculcates poor service delivery and hampers growth when public funds are embezzled.
He also mentioned that poor governance and weak systems prone to manipulation have been a major challenge to devolution.
At the same time, Wako said illiteracy among some members of the county assembly is hampering devolution as it scuttles oversight.
"Other serious challenges include low level of education of some MCAs and failure to strictly implement laws on anti-corruption and management of public resources," he said.