Around 13 such coaching centres were sealed during the action till late Sunday night, it said.
These included IAS Gurukul, Chahal Academy, Plutus Academy, Sai Trading, IAS Setu, Topper's Academy, Dainik Samvad, Civils Daily IAS, Career Power, 99 Notes, Vidya Guru, Guidance IAS, and Easy for IAS.
"These coaching centres were found to be operating in basements in violation of rules and they were sealed on the spot and notices were pasted," the statement said.
The Rau's IAS Study Circle, where the flooding incident took place on Saturday, has been sealed by the police.
The MCD had last year conducted a survey of such coaching centres after a massive fire broke out at an institute in Mukharjee Nagar, another coaching hub, in north Delhi.
"To begin with, the survey will be used to identify those flouting norms," the official said.
Three civil services aspirants -- two females and a male -- died after a library housed in the basement of Rau's IAS centre got inundated following heavy rains Saturday evening, and reportedly led to the failure of the single biometric entry and exit point.
"A gross criminal negligence is found on part of the owner of the institute in ensuring safety measures as the library in the basement was running illegally and had only one entry and exit point that was biometric-enabled and got locked due to the flooding," the MCD official said.
"The students could have escaped had the exit been free. The MCD only approves the building plan but if somebody misuses the basement for commercial activities after declaring it will be used for parking and storing purposes, what else can the agency do to ensure protection?" he said.
The official said storm drains in the area, which carry excess rainwater to bigger drains, were covered by "encroachers on street sides" and contributed to the flooding.
"Delhi Mayor Shelly Oberoi has held a meeting of the officials in this regard and setting up of a high-level committee after talks with the Delhi government will be announced soon," another official said.�