Hans Christian Wolters on Monday said prosecutors had some evidence Madeleine was dead but not enough for a trial.
But in a U-turn just five days later he has backtracked on that comment, saying there is no forensic proof to support his claim.
Mr Wolters told the Sunday Mirror he did not realise “it was so important” to the British public when he said police were working on the assumption Madeleine was dead.
“Because there is no forensic evidence there may be a little bit of hope [that she is alive],” the spokesperson for the Braunschweig public prosecutor’s office told the paper.
“We don’t want to kill the hope and because there is no forensic evidence it may be theoretically possible.
“I know it’s important for the British people when I say she is dead, but I did not know it was so important.”
The probe into Madeleine’s disappearance from Praia da Luz, Portugal, in May 2007 has been thrust back into the limelight after authorities announced they were investigating a 43-year-old convicted German paedophile.
The suspect, who is currently serving a prison sentence, has been named in reports as Christian Brueckner.
Brueckner is known to have lived on the Algarve coast between 1995 and 2007 and his Portuguese mobile phone received a 30-minute phone call in Praia da Luz about an hour before Madeleine, then three, vanished from her family’s holiday apartment on 3 May 2007.
Madeleine’s mother Kate went to check on her during a meal with friends at a nearby tapas restaurant but found the window open and her oldest daughter missing from her bed.
Speaking to The Sunday Times, Mr Wolters said prosecutors were investigating whether a hotel employee may have helped the suspect target the McCanns’ apartment knowing they were out at a restaurant.
There is no suggestion the member of staff knew about Madeleine’s kidnap in advance, and Mr Wolters said: “The phone call made by the suspect could be between him and a member of staff who told him when to break into the McCanns’ apartment.”
He added that police had not interviewed Brueckner about Madeleine’s murder at the time as they had not traced the person who called him.
Mr Wolters told the paper: “The person he spoke to could put the phone in his hand [by confirming it was Brueckner to whom he spoke], which would mean he was in the area at the time.
“This is the evidence we want before we issue an arrest warrant and then interview him for the murder. It would help the case against him – but we would also need more evidence.”
Scotland Yard said it received nearly 400 tips to its Operation Grange team in the days after the renewed appeal.
Operation Grange refers to the force’s active investigation, which is still classed as a missing person inquiry because there is no “definitive evidence whether Madeleine is alive or dead”, a police spokesman said.
Additional reporting by PA
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