Arvind Kejriwal blamed Prime Minister Narendra Modi for the "raid", calling him a "coward and a psychopath".
"When Modi couldn't handle me politically, he resorts to this cowardice," he added.
Officials from the Central Bureau of Investigation (CBI) have denied the allegations.
"It is not a raid on Arvind Kejriwal's office, it was a raid on Rajender Kumar, principal secretary to the CM [chief minister]," CBI spokesperson Devpreet Singh told BBC Hindi.
However, Mr Kejriwal has accused the CBI of "lying".
India's Finance Minister Arun Jaitley told the upper house of parliament that the "raid has nothing to do with Mr Kejriwal".
Parliamentary Affairs Minister Venkaiah Naidu added that it had become a "fashion" for Mr Kejriwal to blame the prime minister.
Mr Kejriwal's local government has been locked in a tussle for power with the federal government since he was elected to power in February.
Unlike in much of India, Delhi's Aam Aadmi Party (AAP)-run local government does not have absolute administrative powers over the state. Control of the state's police force, land, and law and order rests with the BJP-controlled federal government.
The AAP has consistently campaigned for greater autonomy for the state, and its tenure has been peppered with confrontations.
Party members have tweeted, calling it the "darkest day in democracy".
The chief minister of India's capital, Delhi, has alleged that his office has been raided by the country's federal investigation agency.