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The CBI says that Mr Kumar was the driving force of a 50-crore scam involving the government in 2006. Another bureaucrat, Ashok Kumar, was also arrested along with the two owners of a firm that allegedly landed sweetheart deals.
The Delhi government has described the arrest as an attempt by the Centre "to paralyze the Chief Minister's office".
Mr Kumar's offices were raided in December 2015 by the CBI. At the time, Mr Kejriwal controversially described the Prime Minister as "a psychopath".
"Mr Modi, even if you only leave us with just peons, we will run the government with them," said Deputy Chief Minister Manish Sisodia today.
The clash over the senior-most bureaucrat in the Delhi government is part of the continuing hostilities between Mr Kejriwal and the Centre, who he accuses of illicitly trying to run Delhi through decisions that undermine his authority.
The CBI's case against Mr Kumar is that in an earlier term with the government, he manipulated processes to deliver contracts for computers and software to firms. They say that bribes amounting to three crores were paid to senior government officers including Mr Kumar.
The CBI says that Mr Kumar was the benami or proxy owners of these firms.
Both Mr Kumar and Mr Kejriwal are IIT alumni.
Mr Kumar began his career with the Delhi government in 1991. Mr Kejriwal picked him as his top advisor even during his famously short 49-day term which ended with a resignation that the Chief Minister later apologized for.
Last month, the Centre refused to clear all 14 bills or proposals for new laws that had been passed by the Delhi Assembly, including Mr Kejriwal's pet plan for a Jan Lokpal or ombudsman to combat corruption among government officers.
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