It was commissioned after Kettering General Hospital admitted "anomalies" with its waiting lists data.
The report said patient safety was seriously jeopardised and cost-cutting contributed to the problem.
A whistleblower claimed patients were removed from lists to help meet national targets, but investigators found no evidence of fraud.
In May, the BBC reported allegations by David Phelan, who was also a trust governor at the time, that data had been "fiddled" .
A hospital review found that 138 patients were harmed - including one who had substantial sight loss - as a result of the long waits.
The hospital admitted using "inappropriate filtering" of its data to remove patients but denied it was a deliberate attempt at making figures look better to avoid fines.
A report, written by consulting company CPA, concluded that "flawed methods were used to extract waiting time data" between 2006 and 2015, and raised questions over whether the trust was "misled" by executives and deputies, or whether the individuals "lacked the understanding, judgement or competence to appreciate the position".
It also described the decision to cut administration staff as "misguided" and said investigations into whether patients had been harmed "lacked rigour".
Report author Chris Anyan said most staff he had spoken to knew about the problems "for some time" but "the significance of these issues was not fully appreciated, including the potential risk to patients".
Kettering General Hospital said it had implemented an improvement plan in response to the report.
In a statement, the trust said: "The review conclusively demonstrates that the root cause of our problems were a number of historic failings which together affected the accuracy of our waiting times data.
"The report also found that senior managers who had been trying to address our problems and produce accurate information were 'well intentioned' but failed to recognise the scale and significance of the waiting time issues."
A hospital may have lost track of its patients for almost a decade, according to a report obtained by the BBC.