Metropolitan Police chief Sir Ian Blair has apologised to the parents of Holly Wells and Jessica Chapman for comments he made about the Soham murders.
He said his comments that "almost nobody" understood why it became such a big story, had not meant to diminish the significance of a "dreadful crime".
But he said there was no doubt race impacted on the news agenda.
He has been criticised by campaigners and some Metropolitan Police Authority members and media representatives.
Sir Ian's comments came after he told an MPA meeting the media was institutionally racist in its reporting of murders.
He told Radio 4's Today programme on Friday: "I obviously have to unreservedly apologise to anyone connected to the Soham murders, especially the parents of Holly and Jessica for re-igniting this story.
"It was not intended to diminish the significance of this dreadful crime, which is exactly how I described it.
"But... I was responding to a question raised about the differential response to different murders and that led to an entirely legitimate discussion about the difference between investigative needs and news values."
He cited the coverage of the murders of white lawyer Tom ap Rhys Pryce and Asian builders' merchant Balbir Matharu, while conceding there were some exceptions - such as the Damilola Taylor killing.
Sir Ian apologised to Jessica and Holly's parents
But Richard Barnes, a member of the MPA, said people had found the words about the Soham murders "insensitive and shocking" and said Sir Ian needed to clarify his remarks.
Mr Barnes said: "He couldn't understand that this one became the biggest story in Britain - well I can.
"It was two little girls who got murdered, who were missing, who were reported missing for 10 days by their local police."
Mr Barnes said the overuse of the phrase "institutional racism" had begun to devalue the term, and in turn was "beginning to undervalue racism itself".
Dee Edwards, from campaign group Mothers Against Murder, said the comments had been "unfortunate", adding: "It is always big news when a child goes missing".
And former Sun editor David Yelland rejected the idea news organisations were institutionally racist.
MURDER VICTIMS 2001-04
Source: Home Office
England & Wales only
"He is simply wrong... To use that word, to say racist about anybody, particularly people in broadcasting and the media is a very big thing for him to say, a very very big thing indeed, and I think he's way out of line," he told the BBC's World at One.
It is not the first time Sir Ian has courted controversy.
His remarks after police shot dead an innocent Brazilian man they mistook for a suicide bomber, are the subject of an Independent Police Complaints Commission.
And he was accused of being too politicised after lobbying MPs ahead of a vote on holding terrorism suspects for 90 days without charge.
But on Friday he was backed by Mayor of London Ken Livingstone, Labour peer Lord Harris, the MPA's chairman Len Duvall, a former MPA chairman and deputy chair Cindy Butts, who said he was right to raise the issue.
Mr Duvall said: "Thomas Rhys Pryce's murder was tragic and horrific, but so were the other heinous murders committed at that time.
"The question remains as to why just one of these horrific crimes received mass media coverage."