They said the cash, hidden in various wooden cavities of furniture and other items, was recovered and seized from the Delhi premises of a broker identified as Sanjay Gupta.
Gupta did not reply to queries sent by PTI. His phone as well as that of his family members were switched off.
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Besides Delhi, searches were also conducted at Mumbai, Kolkata and Bengaluru.
"Certain other incriminating documents have also been seized. The raids are still on," a senior official said.
The department has been conducting searches in Delhi and Mumbai on few brokers linked to the NSE for the last three days and the tax sleuths have said they recovered a number of documents and computer peripherals till now.
The premises of Chitra Ramkrishna, former MD and CEO of the exchange, as also that of others formerly associated with NSE were also searched, they added.
There was no immediate response to query sent to Ramkrishna.
In the NSE co-location case, certain brokers, including Gupta's OPG Securities, operating on its trading platform allegedly got preferential access to servers of the exchange.
A co-location facility provides early login and faster access to data feed of the exchange. Even a split-second faster access can yield huge gains for a trader.
The NSE and brokers being raided by the department have not commented on the action till now.
Officials had said the action is based on "actionable inputs" suggesting tax evasion by a few entities linked to the NSE and also the co-location issue, where it is alleged that certain brokers operating on the trading platform allegedly made abnormal profits as a result of getting preferential access to the servers of the exchange.
The co-location case is under the scanner of Sebi while the National Stock Exchange (NSE) earlier this week had submitted the forensic audit report on the issue, prepared by auditing firm EY, to the markets regulator.
EY was entrusted with carrying out the forensic audit into cash markets, currency derivative and interest rate futures platform.
The nation's largest bourse had earlier engaged Deloitte for a forensic audit of its equity derivatives platform.
In July, the NSE had approached the Securities and Exchange Board of India (Sebi) to settle the case through consent mechanism. The regulator has not responded to the proposal as yet, though.
The controversy has delayed NSEs IPO plans. Its rival BSE already went public in January.