"The man confessed overnight that he had also killed Elias," said Berlin police spokesman Stefan Redlich, referring to a six-year-old German boy who had been missing since July.
Investigators were combing through a garden allotment for Elias' body after the man identified as Silvio S said his corpse was buried there.
An AFP photographer at the scene saw police transporting a body away from the allotment.
The suspect was arrested yesterday after his mother told police he may have been involved in the kidnapping of the Bosnian boy, Mohamed.
An eight-hour autopsy confirmed the body was that of Mohamed, prosecutors said today.
The boy had been missing since October 1, when his mother took him and his sisters to Berlin's main refugee registration centre, Lageso, which receives hundreds of asylum seekers daily.
His disappearance triggered a massive police operation, with the missing child's photo appearing regularly on television screens in Berlin's subway trains.
Police also released CCTV footage of a bearded man leading a child who was holding a stuffed toy.
Forensic investigators found signs of strangulation on Mohamed's neck, prosecutor Michael von Hagen said yesterday, adding that the accused had admitted using a belt to choke the child to death.
The man, who worked as a security guard in Berlin, admitted taking Mohamed from the refugee centre to his flat where he sexually abused him, von Hagen said.
But when the child began squealing, the suspect killed him to prevent anyone from hearing, before hiding the body in cat litter to hide any odour, the prosecutor said.
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