The outspoken governor is under the EACC spotlight over alleged corruption in a number of his county programmes, including Kaa Sober, which was aimed at rehabilitating alcoholics.
Mr Waititu has also been questioned over his recent property acquisitions, including that of a building located within Nairobi’s central business district.
The raid comes as EACC intensifies the fight against corruption in the devolved units.
Kiambu Governor Ferdinand Waititu has been arrested in Nairobi as the anti-corruption watchdog investigates corruption in his government.
Detectives from the Ethics and Anti-Corruption Commission (EACC) took away the outspoken county boss after more than six hours of interrogation and search at his Runda home.
The crime busters raided the residence and the governor's offices a few minutes after 5am and started a search for files and documents.
The tens of officers camped at the home until noon when they arrested the county boss, who was restrained from leaving for work, and took him to Integrity Centre, the operations nerve centre of the EACC.
The detectives carted away files and records relating to contracts issued by Mr Waititu’s administration.
They also confiscated and carried away some number plates and documents which were found in the boot of his Toyota Prado.
Neither Mr Waititu nor EACC detectives addressed a battery of journalists who camped outside the besieged home as the raid went on.
The outspoken governor, popularly known as Baba Yao, is under the EACC spotlight over alleged corruption in a number of his county programmes, including Kaa Sober, which was aimed at rehabilitating alcoholics.
In a statement, EACC said it was investigating claims of irregular award of tenders worth Sh588 million to companies associated with Mr Waititu and members of his immediate family.
"Preliminary investigations show that contractors paid monies to senior county officials, their companies or relatives through proxies," the statement reads in part.
The governor is also on the spot over alleged fraudulent acquisition of public funds, conflict of interest and money laundering.
"During the searches, valuable evidence relevant to the investigations was recovered," the EACC said.