A source involved in the raid said the Commission was investigating the governor following reports of alleged involvement in irregular payment of allowances and awarding of tenders.
The investigations also involve alleged allowances for fictitious foreign trips.
Officials from the Ethics and Anti-Corruption Commission (EACC) conducted a raid on Governor Anne Waiguru's rural home at Kagio village, Kirinyaga County.
The officers went to her home at 6am on Thursday and ransacked it for hours, in search of crucial accounts documents.