The Surrey force's investigation had been described as "chaotic and aimless" by an independent police inquiry, according to the Sunday Mirror.
It reports that the head of the inquiry, Detective Inspector Stuart Gibson, was replaced by Detective Inspector Brian Marjoram, an expert on paedophiles.
Amanda Dowler, a 13-year-old also known as "Milly", disappeared while walking home from the train station at Walton-on-Thames on 21 March.
The newspaper says the Sussex Police inquiry into the handling of the case was "highly critical" and "made it clear that urgent and dramatic changes needed to be made".
The paper reported that mistakes made by the force included taking more than a month to carry out a detailed forensic examination of Milly's clothing, failing to treat her disappearance from the outset as a potential murder inquiry and waiting weeks to examine her computer.
Surrey Police has rejected this and said the force had always treated the case as a "serious and critical incident".
It said in a statement: "It is standard procedure with an inquiry this size for other forces to be requested to review the work of the investigation team.
"In this case Sussex Police was asked to conduct those reviews.
"The first review has been completed and concluded that: `This is a well run inquiry which despite an immense amount of effort by Surrey Police has failed to find the missing child Amanda Dowler, or provide any evidence to positively indicate what might have happened to her'."
The statement said team morale remained high despite the long hours being worked and the force stressed that officers were determined to establish what happened to Milly.
The police added: "Detective Chief Inspector Stuart Gibson has demonstrated a huge commitment to the inquiry.
"DCI Gibson is also the divisional senior detective for North Surrey Division.
"North Surrey is one of Surrey's busiest divisions and the return of DCI Gibson to his divisional duties is related directly to the support required on that division.
"DCI Brian Marjoram has joined the team leading the investigation and is not a direct replacement for DCI Gibson.
'Staying positive'
"It has been essential throughout the investigation that we deal with fact and evidence and not with speculation and rumours."
Milly's mother, Sally, said last week that they were trying to stay positive for the sake of the missing teen's sister Gemma.
She expressed surprise that nothing had been uncovered and said: "When Milly first went missing we would never have believed that we would have had no news of her by now."
A Surrey Police spokesman said on Sunday: "It is an extremely unusual incident for a girl to go missing without a single clue or lead to help the investigation team.
"Regardless of how the investigation is technically classified, the same meticulous, painstaking and thorough approach would have been taken."
Two men have been arrested and released on bail without charge in connection with Milly's disappearance.