Ethics and Anti-Corruption Commission detectives have frozen 13 accounts belonging to prominent businesspeople in Kilifi county.
They believe at least Sh50 million cannot be accounted for.
Several county officials, among them chief officers are being investigated.
County departments reportedly involved in massive corruption include ICT, education, public service and health.
Officials who spoke to the Star on condition of anonymity said senior officials had their accounts frozen.
"We have been wondering when will this come to an end. They seem not to be worried. At times they supply nothing to the county yet they end up being given all relevant documents," a source said.
The Star has established that some individuals whose accounts have been frozen are from outside the county.
Some affected businesspeople are seeking court orders to overturn the decision.
Those who spoke to the Star said they are being targeted unfairly.
"We are small fish in the business. They could have targeted top officials at the county level. Why have they been spared," a businessman said.
Malindi EACC boss George Ojowi said no one will be spared regardless of the power they yield.
He said investigations have started.
"We are already in court. These guys have swindled millions of county money. It is going to be a lesson to some members. We will ensure the whole amount is recovered," Ojowi said.
He said EACC is investigating claims some prominent politicians are involved in conning.
Ojowi urged the public to share information with the authorities.
"Several people were conned during the just concluded Malindi by-election, but once they reported the incidents, they disappeared," he said.
