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".

Cooke won the first of GB's gold medals at Beijing in 2008, but since then Lizzie Armitstead has taken over as team leader.
That means Cooke could have to sacrifice gold to Armitstead, with whom she has had differences in the past.
But Cooke said recently: "I know deep down what it takes to win races."
In an interview recorded for Wales at the Olympics, Cooke, who is now based in Switzerland, added: "I have proven through my experience and my results what I'm capable of."
Cooke and Armitstead's relationship was strained at the 2011 World Championships in Copenhagen.
They were in the same GB women's team, with Armitstead the leader.
The team looked well-placed to contend for the title until a crash late in the race separated Armitstead from Cooke up ahead.
They have differing recollections of subsequent events, which saw Cooke set off for the line only to finish fourth, with Armitstead coming home seventh.
Matters came to a head when Armitstead told Cycling Weekly magazine of a furious row once the team had crossed the line, adding: "I've never seen her [Nicole] work for a team-mate. It was a unanimous decision that Nicole didn't do her job properly."
But Cooke says that the pair have now smoothed over their differences ahead of the Olympic road race in London on 29 July.
"Lizzie and I have spoken about what happened in the race [2011 World Championships], what's happened since. I have forgiven for what she did and how she reacted," insisted Cooke.
"And I think in a way it did highlight why we were under-performing as a team.
"We realised that if we went into the London Olympics like we went into the last World Championships we would probably under-perform again."
The chief minister of India's capital, Delhi, has alleged that his office has been raided by the country's federal investigation agency.
[NEXT_CONCEPT]
Welsh cyclist Nicole Cooke is in the UK for Sunday's Olympic road race with team orders likely to hinder her chances of another gold medal.