However, it became the subject of controversy following various allegations relating covert operations, secrecy and absence of defined accountability, and the conviction of an assistant director for serious criminal activities.

Headed by retired Supreme Court justice David Patten, the Inquiry handed its report to the Government on 30 November 2011.

It found no evidence of misconduct or impropriety other than that of the assistant director, whose arrest and conviction could not have been achieved without the investigative work of the Crime Commission.

The first chairman of the State Drug Crime Commission (SDCC) was Judge John Lloyd-Jones, who was replaced after only four weeks following objection by the legal fraternity to the principle of a judicial officer's presiding over an investigative body.

PIC investigations revealed that the commission and lawyers acting for alleged and convicted criminals negotiated legal costs, sometimes in an extremely short timeframe.

The controversy expanded as the commission was accused of undermining free speech by demanding records and phones from Fairfax journalists.

On 11 August 2011, after a five-month trial, a NSW Supreme Court jury found former NSWCC assistant director Mark Standen guilty of conspiring to import and supply 300 kilograms (660 lb) of pseudoephedrine, a chemical that could produce A$60 million worth of "ice", or crystal methamphetamine.

[13] On the same day of Standen's conviction, the NSW Government announced that a Special Commission of Inquiry would be conducted into the affairs of the NSWCC.