Karen Kneller was director of casework when the miscarriages of justice body did "very poor" work on Malkinson's first application to overturn his conviction for a 2003 stranger rape he did not commit.
Kneller was promoted to chief executive in 2012, shortly after Malkinson's application was rejected for the first time. Last year she was awarded a bonus and pay rise while Malkinson was struggling with unemployment in the aftermath of spending 17 years in prison.
A review published this week found Malkinson could have been exonerated almost a decade earlier if the CCRC had properly understood the significance of new DNA evidence when he first applied.
Malkinson said: "If accountability means anything, it means [Kneller] has to go, as does the rest of the CCRC's leadership team who have presided over an organisation that is simply not doing its job."
While Chris Henley KC's review contained personal criticism of the watchdog's chair, Helen Pitcher, for failing to apologise and for "taking too little responsibility", Kneller's role has not been examined.
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