Mohamed Januzi disappeared on Oct. 1 while waiting outside the offices of the government program for social care with his mother and two siblings.
Police had released video footage showing the alleged abductor walking hand-in-hand with Mohamed away from the offices.
"These videos led to relatives of the suspect coming forward," police spokesman Thomas Neuendorf said. "In the man's car, a child's body was found."
Neuendorf said police were waiting for the results of an autopsy to confirm the child's identity as well as the circumstances around his death, including when he may have died.
Initial evidence shows there is no indication that the suspect and the child knew each other, he said.
Daily Bild reported that Mohamed's family came to Germany from Bosnia.
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