The inquiry will investigate the role of Greater Manchester police (GMP), the Crown Prosecution Service (CPS) and the Criminal Cases Review Commission (CCRC) in his conviction and subsequent attempts to overturn it.
Malkinson and his civil lawyer expressed concern that it would not be statutory, meaning witnesses will not be compelled to give evidence and there would be no legal obligation to disclose documents.
Malkinson, 57, was convicted in 2004 of a rape in Greater Manchester despite there being no DNA evidence.
Having spent almost two decades trying to convince the authorities he was innocent, the court of appeal overturned his conviction last month after fresh DNA testing linked another man to the crime.
The CCRC had previously announced a review of its handling of his case after it twice declined to order further forensic testing or refer the case for appeal, but Malkinson has been calling for a full independent inquiry.
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