Nairobi County Secretary Pauline Kahiga was on Tuesday arrested at City Hall by Ethics and Anti-Corruption Commission (EACC) operatives.
The dramatic arrest took over an hour as the EACC detectives tried to penetrate barricades put up by City Hall guards.
Reporters at the scene were also kicked out by the county security officers as they tried to document the events.
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Governor Sonko accompanied by County Secretary Pauline Kahiga during a past appearance at Parliament (Twitter)
Ms Kahiga was later led out of her office and into one of the vehicles EACC officials had arrived in and some documents were carried out of her office.
EACC explains County Secretary Kahiga's arrest
EACC spokesperson Yasin Amaro explained that the county official had been accused of hiding crucial evidence that could uncover corruption at the county offices.
Governor Mike Sonko is himself under probe by EACC over the source of his wealth.
The office of the county secretary is the central point for all major county operations by the county's executive administration as well as acting as the secretary to the county cabinet.
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Nairobi County Secretary Pauline Kahiga
Ms Kahiga's predecessor, Peter Kariuki, was fired by Governor Sonko after he defended Pumwani Hospital workers during the infant corpses debacle.