The officers had first raided his office at City Hall but did not find him. They only took away some crucial documents and asked his secretary to accompany them.
“They arrived at around 2pm and stormed the office. They carried documents, huge files and cash money amounting to about a million shillings,” said a county employee, who did not want to be identified.
It is not until Wednesday night that the EACC detectives managed to get Mr Wainaina from his house in Kiambu County.
According to City Hall insiders, the chief of staff is alleged to have amassed a lot of wealth since assuming office in 2013.
He is reported to have checked in at work at around 10am on Wednesday morning and left shortly.
“He came and he is lucky the EACC came when he was not there. Come see his office, it’s in a total mess,” said the county worker.
Mr Wainaina is expected to be charged with corruption before a Nairobi court on Thursday.