The searches were carried out at the premises of Ms Aastha Minmet India Pvt Ltd and Ms Juggernaut Projects Ltd in Mumbai, Bangalore and few other places, sources said.
Both the firms, according to sources, are major defaulters in the NSEL case owing investors over Rs 250 crores.
Documents related to business operations have been seized and the searches will finish by tomorrow, they said.
This is the second such action by the central agency in this case.
Investigations by the agency, probe reports said, have revealed that funds received from NSEL were diverted by the firms (which were searched today) for investments in real estate, plant capacity expansion, repayment of loans and purchase of high end vehicles.
Real Estate investments of the groups are located in Mumbai, Thane, Navi Mumbai and other parts of the country and the firms are suspected to have executed contracts by launching on the stock exchange portal without the delivery of any physical stock of TMT bars in the NSEL warehouses and funds were diverted.
The agency, which is probing alleged financial irregularities at the bourse, is probing the case alongside the Economic Offences Wing of the Mumbai police.
ED has earlier raided another firm involved in the stock exchange-- Mohan India and its concerns-- and has attached properties worth Rs 100 crore under the Prevention of Money Laundering (PMLA) laws.