However, the city's Deputy Police Commissioner Dhananjay Kulkarni said that the department was conducting a "transparent and fair investigation".
"There is no question of sparing anybody. We have been initiating action against all those involved based on whatever evidence is emerging during the probe. One should not be sceptical about the investigation," said Kulkarni, who is also city police's spokesperson, while reacting to the allegation.
FTIL did not comment on the allegations.
The spot exchange has recovered only Rs 371.8 crore from defaulters as on March 30 this year.
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In a letter to the Mumbai Police Commissioner, NSEL Investors' Action Group (NIAG) -- which has about 400 members -- has alleged "shoddy investigation".
Citing various instances of the investigation team being "purposely going soft" on FTIL and various other accused, it said: "This clearly shows that somebody from Mumbai police is still protecting Jignesh Shah/FTIL and Rawal group in NSEL scam."
"Your SIT (Special Investigation Team) has not yet purposely investigated/interrogated Rawal Group who traded on NSEL for Rs 1,352 crores and withdrew all their funds before the scam broke," the action group alleged.
To safeguard the interest of investors and creditors, the Corporate Affairs Ministry last year had proposed a merger of the NSEL with Financial Technologies India Ltd (FTIL). The draft order for the merger has, however, been opposed by FTIL.
Meanwhile, Corporate Affairs Ministry last week finalised the share swap ratio for the proposed merger of crisis-hit NSEL with its parent FTIL, which itself will not get any share.