Led by Baroness O’Loan, the Daniel Morgan Independent Panel accused the Met of ignoring or hiding corruption and flaws in the case for three decades to protect its public image.
He also accused the force of delaying his work by not delivering the documents on time.
However, while Scotland Yard accepted some findings, it rejected the charge of institutional corruption.
In response, he said: “We accept that corruption was a major factor in the failures of the first investigation, but we do not accept that we are institutionally corrupt as has been suggested.”
He added that he was working hard to “root out corruption.”
In May, the Metropolitan Police admitted that documents relating to the murder investigation had been found in a locked cupboard which should have been handed over to the inquiry.
A total of 60 documents, comprising more than 150 pages, were discovered at Scotland Yard in January in a cabinet that had not been opened for several years.
Deputy Commissioner Barbara Gray said at the time that the force fully recognized “how unacceptable and deeply regrettable this situation is.”
“We are working to understand what has occurred and any impact. We apologize to the family of Daniel Morgan and to the Panel,” she said.