An eight-year probe found corruption and the “irretrievable” loss of evidence through poor investigative practices had prevented the killers of Daniel Morgan from being brought to justice.
An independent panel said that although its investigation focused on historic failures stemming from the 1987 killing, the term institutional corruption was used “in the present tense”.
Mr Morgan’s family called for commissioner Dame Cressida Dick to consider resigning after she was personally criticised over the disclosure of evidence to the panel.
At a press conference on Tuesday, assistant commissioner Nick Ephgrave said his superior did not have “any need to consider her position”.
“She has overseen disclosure to a level that has never been done before,” he added.
“The access the panel have had has been unparalleled in my experience.”
Dame Cressida did not appear at the press conference but issued a written statement saying the failure to bring Mr Morgan’s killers to justice was a “matter of great regret”.
“Our mistakes have compounded the pain suffered by Daniel’s family - for that I apologise again now,” she added.
The commissioner insisted she had been “personally determined that the Met provided the Panel with the fullest level of co-operation in an open and transparent manner, with complete integrity at all times.”
She added: “I recognise this is a powerful and wide-ranging report. We will take the necessary time to consider it and the associated recommendations in their entirety.”
The Metropolitan Police has commissioned a new forensic review of evidence in the case to look for new opportunities, and is offering a £50,000 cash reward for information leading to the successful prosecution of those responsible for the murder.
Mr Ephgrave said the failure to solve the murder was a “matter of deep regret” and apologised to Mr Morgan’s family for “amplifying their pain”.
He said that Scotland Yard acknowledged that “corruption on behalf of a number of officers in the early stages of the inquiry hampered the investigation”.
However, he rejected the panel’s label of “institutional corruption” and said he did “not see evidence that supports that assertion”.
“I don’t accept the Metropolitan Police Service is institutionally corrupt in the broadest sense,” Mr Ephgrave said.
“It doesn’t reflect what I see every day. That isn’t to say we have not made many mistakes over 34 years and many errors, or that people have not fallen short of the standards we expect, or done things we don’t want them to do.”
The senior officer said the Metropolitan Police had improved the way it dealt with corruption and had one of the largest anti-corruption units in the UK.
The report said that severe failings in the initial investigation into Mr Morgan’s death, when there were immediate suspicions over the involvement of corrupt police officers.
The panel found the crime scene was not searched, interviews were not properly carried out and suspects were forewarned of their arrests, meaning potential evidence had been “irretrievably lost”.
It criticised the 1988 inquest into Mr Morgan’s death, finding a coroner was “inaccurate” to say there was no evidence of police involvement in the murder.
The home secretary told MPs she had written to the commissioner requesting a “detailed response” to the panel’s recommendations, and asked HM Inspectorate of Constabulary to look at the issues raised.
Mr Ephgrave appealed for anyone with information to come forward by calling a dedicated information line on 0203 276 7816 or contacting Crimestoppers anonymously on 0800 555 111.