The Chief Minister, who broke the news of raids on Twitter, accused the Modi government of resorting to vendetta politics and came down heavily on the CBI for the raids at Players Building, which is home to the offices of the Delhi secretariat in central Delhi.
"CBI raids my office," Kejriwal tweeted.
"When Modi cudn't handle me politically, he resorts to this cowardice. Modi is a coward and psychopath," he said in another tweet expressing his anguish over the raids.
A CBI Spokesperson, however, said the searches were being conducted at the office of the Principal Secretary Rajendra Kumar. Searches were being conducted at 14 locations, the spokesperson said, but did not give details.
The BJP also hit back at Kejriwal with Union Minister Prakash Javadekar saying the CBI was only probing a complaint of corruption against an officer and maintained it has nothing to do with Kejriwal's office.
CBI sources said that a team of its officials went to the Delhi Secretariat, which houses office of Kejriwal and other ministers in the morning and conducted the search in the third floor of the building.
The CBI said it has registered a case against Rajendra Kumar on allegations of abusing his official position by "favouring a particular firm in the last few years in getting tenders from Delhi government departments."
"After taking warrants, searches are being conducted in the office and residence of Rajendra Kumar. The allegations against Rajendra Kumar were raised by Ashish Joshi, former Member Secretary, Delhi Dialogue Commission," the agency said.
The third floor of the secretariat also houses Kejriwal's office.
The AAP government has been locked in a running feud with the Centre over the control of important functions like law and order, police and land.
Delhi Government and AAP reacted angrily to the "raid".
calling it a "darkest" day and "undeclared emergency" in the history of Indian democracy.
Deputy Chief Minister Manish Sisodia claimed the Centre was controlling the CBI and claimed the raid at Rajendra Kumar's office was aimed at sending message to officials "if they worked with Kejriwal honestly, they will be troubled."
"If Modi ji wants to send a message amongst officials who are working that if you work along with Kejriwal honestly, then they will be targeted, then it is a very dangerous message. This will have opposite effect," he warned.
Another AAP leader Ashutosh said CBI is "lying to the teeth" for saying that the office of the chief minister was raided and attacked Modi.
BJP condemned Kejriwal for the kind of language used to criticise Modi and said it was "absolutely unacceptable".
"Does he want to protect the corrupt?," Javedekar asked, adding, "Instead of taking action against the corrupt, he is accusing the prime minister. This is absolutely unacceptable.