The decision to freeze the shares was taken after the ED conducted searches on 10 premises in Delhi, Mumbai and Hyderabad last week.
ED in a statement said that during the course of probe in the case, an amount of 28 million Euro (Rs 214 crore approx) was paid to Guido Haschke and Carlo Gerosa, the two alleged middlemen in the Rs 3,600 crore deal, through a Tunisa-based company.
Officials said the agency has also seized a number of documents and computer hardware after the searches.
It added that it "unearthed the evidences of transfer of funds" after the searches and hence now it has issued orders to freeze shares of certain firms worth Rs 86.07 crore that are located in the three countries.
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The freezing of assets (shares) has been done under the Prevention of Money Laundering Act (PMLA).
He is the third middleman, apart from Haschke and Gerosa, who is being investigated by both the Enforcement Directorate and the CBI.
ED had registered a PMLA case to probe this deal in 2014 and named 21 people, including former IAF chief S P Tyagi, in its FIR.
It had also arrested Delhi-based businessman Gautam Khaitan in the case, who is out on bail now.
It had earlier submitted (as part of its first charge sheet) that Khaitan was on the board of Aeromatrix, a Chandigarh-based company that was allegedly a front firm for the financial dealings in the chopper deal.
The ED and the CBI had issued Letters Rogatory (judicial requests) to multiple countries to gather more leads and evidences in this case.