Hundreds of workers may be sacked after it emerged they were illegally employed.
Reports say some senior county government officials took advantage of the leadership vacuum at the County Public Service Board to hire workers without the knowledge of the executive.
The board does not have a chief executive officer or a chairman despite the central role it plays in the management of human resources.
Former chairman David Kombo was elected county assembly speaker while the CEO, Charles Nyakeri, is battling a court case after he was sent on compulsory leave.
Board member Carolyne Nyaseti was appointed chief officer for Youths, Sports and Social Services.
Laying off the irregularly hired workers will help Governor James Ongwae to cut the growing wage bill.
In her latest report, Controller of Budget Agnes Odhiambo lists Kisii among 35 counties whose expenditure on personnel emoluments was too high.
Unless measures were taken, she said, these counties would soon find it hard to sustain themselves.
Kisii is said to be spending at least 52 per cent of its resources on staff salaries.
In his end of year speech, Mr Ongwae ordered the county secretary and head of public service to conduct a headcount immediately to establish the number of workers his government was paying.
But just before the exercise was concluded, Ethics and Anti-Corruption Commission (EACC) detectives raided the County Public Service Board offices and the Human Resource Department a week ago.
The officers took away several computers and documents and said they were investigating the irregular hiring of workers, especially towards the August 8, 2017 General Election.
“We undertook a search and obtained important documents that will assist our investigations into irregular recruitment of staff,” said EACC Deputy CEO Michael Mubea.
The Standard has established that some senior county government officers have been colluding with the employing officers to issue fake appointment letters to unsuspecting individuals without the knowledge of the county executive.
Some of the officers have already been sent home as investigations continue.
The governor said EACC was at liberty to investigate the allegations "because that was part of their mandate".
“I am aware that some people could have been employed during the campaign period. Some people may have taken advantage of my busy campaign schedule and issued illegal employment letters. The headcount will be completed in a few days and all those issues will have been sorted,” said Ongwae.
“Some people want to politicise the matter and in the process imagine they can gain mileage. We are firmly in control and nobody should be allowed to distract us from delivering our campaign promises,” he added.
"During my first term in office, I was careful not to interfere with staff because of the prevailing clan politics. This won't be the case anymore. I want to leave a legacy. Get ready to be replaced if you show signs of incompetence. I will deal decisively with anybody who tries to interfere with my efforts to leave a lasting legacy."
Last week, there were indications some staff seconded to the county government could be headed back to their former work stations.