Anti-graft agency detectives on Tuesday raided homes of Governor Okoth Obado in Nairobi and Migori counties.
The Ethics and Anti-Corruption Commission (EACC) officers also raided the Migori County government offices.
A team from Nairobi also camped outside Mr Obado's office but the county boss is currently in his Nairobi home.
Senior staff at the county administration have avoided going into the offices fearing arrests.
"We are here for a major operation...You will see what happens," said one of the EACC detectives.
Some of the county administration's chief officers and directors have recorded statements with EACC on corruption matters.
Several others have been charged and their cases are still ongoing.
Details are scanty on what the EACC officers are looking for but they have been investigating the governor over corruption-related issues.
Earlier this month in an affidavit filed in court, the watchdog claimed that Mr Obado used proxies among them his relatives to siphon Sh2 billion from the coffers of the county government.
EACC claimed that the companies registered by proxies transacted Sh1, 971,179,180 deals exclusively from the county government in a period of three years.