Milly Dowler's voicemail messages were "most likely" deleted automatically, the Metropolitan Police says.
It told the Leveson Inquiry it has no evidence journalists deleted messages on the murdered schoolgirl's phone.
Lawyers for the Dowler family say it is too early to say journalists did not delete messages
Lord Justice Leveson, head of the media ethics inquiry, said he needed police to clarify events because the Met's statement was of significance.
The allegation that News of the World journalists deleted messages first appeared in the Guardian newspaper - and was a turning point in the hacking affair, contributing to the closure of the News of the World and the establishment of the Leveson Inquiry into media ethics.
In a statement to the inquiry, Neil Garnham QC, for the Metropolitan Police, said detectives now thought that Milly Dowler's voicemails had probably been automatically deleted because they were more than 72 hours old by the time her parents got through to her voicemail.
Days after her disappearance, Milly's parents had a moment of false hope when they found they could leave messages on her phone, suggesting to them that their daughter had been picking up previous messages and had deleted them.
Mr Garnham said: "It is conceivable that News International journalists deleted the voicemails, but the Metropolitan Police Service have no evidence to support that."
He said "most likely explanation" was that messages were automatically removed after 72 hours, and added that the network provider had confirmed that this was "a standard automatic function of that voicemail box system at the time".
"I can say from Metropolitan Police Service records that the Metropolitan Police did not tell the Dowlers that voicemails had been deleted, for the simple reason that they did not know of any such deletions," he added.
Phone-hacking detectives have now asked Surrey Police officers, who led the hunt for Milly Dowler in 2002, to give statements.
Confusion over events
The Met's statement to the Leveson Inquiry came amid mounting confusion over exactly what News of the World journalists allegedly did when they accessed Milly Dowler's phone.
Milly's mother Sally Dowler had previously told the inquiry that she had not slept for three nights after detectives told her that her daughter's phone had been hacked.
In an article on Saturday, the Guardian said new evidence had led police to conclude the News of the World was not responsible for the deletion of a specific voicemail from Milly Dowler's mobile phone that had caused her family to have false hopes.
It said News of the World reporters may have inadvertently caused messages to be deleted by listening to them - because the system would then remove them after 72 hours.
But David Sherborne, counsel for the victims of hacking including the Dowlers, questioned the Met's new statement, saying Surrey Police had the name of a journalist who had Milly Dowler's mobile number and Pin.
Mr Sherborne said that there was evidence that someone had continued to access and delete voicemails over a number of days, leading up to the false hope moment - and that there were "only so many culprits".
Glenn Mulcaire, the private investigator used by the News of the World, who was tasked with hacking the phone, has already issued a statement through his solicitor saying he did not delete messages and "had no reason to do so".
Mark Lewis, the Dowler's solicitor, told the BBC: "The 'false hope' deletion might or might not have been done by someone either commissioned, or from The News of the World - so it's too early to say [the newspaper was not responsible].
"What we do know is that The News of the World employees have listened to other messages from Milly which would have triggered an automatic deletion.
"The fingers can be pointed at various people but the fingers have not stopped being pointed for deletion [at] the very people who have hacked into Milly Dowler's phone, so you reach your own conclusions."