Karvy Computershare Pvt Ltd engaged in fraudulent activities with respect to certain initial public offerings in 2005, market regulator Sebi said.
The shares - close to 30% of the total holding - are expected to list on rival National Stock Exchange on or around February 3.
The regulator's concern arises from several recent instances.
Eleven years on, while 80% of scam-hit investors have been fully compensated, more than 50% of the sum is yet to be distributed.