The court on Thursday argued the region where it is located isn’t the last place he lived in Germany and so it isn’t responsible.
The suspect hasn’t been charged in the McCann case, in which he is under investigation on suspicion of murder.
He spent many years in Portugal, including in the resort of Praia da Luz around the time of Madeleine’s disappearance there in 2007. He has denied any involvement in her disappearance.
The suspect, who has been identified by media as Christian Brueckner, is currently serving a seven-year prison sentence in Germany for a rape he committed in Portugal in 2005.
In the German legal system, a court must decide after it receives an indictment from prosecutors whether to take a case to trial.
The Braunschweig state court said its supposed responsibility for the case being in the area had been based on his last residence before going abroad and then to prison.
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But it said that isn’t valid, because the suspect produced evidence of a later residence in the neighbouring state of Saxony-Anhalt, where he was registered as the owner of a property that he kept after going abroad.
The court said that, as a result of its decision, it has lifted a new arrest warrant it issued for the suspect in November. It said in a statement that this has no influence on the suspect’s serving of his current sentence.
It said that its decision can be appealed to a higher court in Braunschweig.
Prosecutors said later Thursday that they will examine the reasons for the decision carefully and then likely appeal.
Fifteen years on, world still searching for answers in Maddie mystery