"The target of this raid was to find something against Arvind Kejriwal," Deputy Chief Minister Manish Sisodia said.
"All files that the CM signed yesterday and was to sign today were in the room that the CBI raided," Mr Sisodia said. "I'm saying categorically... the room that has the Chief Minister's files has been sealed... all affidavits that have to be filed and signed by the CM were there in that room."
The CBI has denied the allegations and asserted that it was searching the office and home of a senior bureaucrat in Mr Kejriwal's office, principal secretary Rajender Kumar, who has been accused of corruption.
Mr Kejriwal targeted Prime Minister Narendra Modi and the ruling party in a series of tweets after the CBI allegedly refused to let anyone into the floor on which the Chief Minister's office is located.
"Modi is a coward and a psychopath," Mr Kejriwal tweeted.
The BJP has demanded an unqualified apology from the Chief Minister, saying his comment was "uncalled for, unwarranted, shameful and condemnable".
Mr Sisodia said there would be no such apology, and said: "You apologise for your actions, we'll apologise for our words."
The CBI has claimed that it found Rs 13 lakh cash in raids on Rajendra Kumar and another person. Rs 2.4 lakh cash and foreign currency worth Rs 3 lakh was reportedly found in Mr Kumar's home.
Union minister Ravi Shankar Prasad taunted the Delhi Chief Minister. "This is a text book case of hypocrisy and double standards. We do due diligence when we appoint secretaries. Didn't you do the same when you appointed him?" he questioned.
Mr Kejriwal and AAP have both defended the officer and said that they trust him.
"Rajendra kumar is an excuse. The real target is Kejriwal," Mr Sisodia said.
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