Officials said the taxman stumbled upon the cases after the department's Kolkata investigation wing, last year, acted against a "large number" of firms and entities dealing in penny stocks in their jurisdiction and few other inter- connected regions.
The probe found share prices of these stocks were "artificially" being raised on the exchanges in order to register "bogus" or fake claims of Long Term Capital Gains (LTCG) or Short Term Capital Loss (STCL).
LTCG or STCL carry tax exemption.
While a senior IT department official refused to give an exact amount of the tax evaded through this modus operandi, he said the figures could be "as much as Rs 500 crore".
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These stocks are prone to manipulation and have been earlier reported by probe agencies and market regulator SEBI to have been used in converting black money into white.
Sources said after "hundreds of" such entities were probed, it was found many of the operatives have businesses across India and are assessed in different regions and hence the taxman has across the country have been asked to conduct a thorough probe against them.
They said while the department will raise tax demands against those who are found in contravention of IT laws, the cases will also be referred to the Securities and Exchange Board of India (SEBI) for action at their end.
It had also suspended trading in shares of as many as 167 companies, while the regulator has written to the Income Tax department in nearly 100 cases where more than 1,800 entities are suspected to have traded in shares valued beyond their disclosed income.