A regional court in the city of Braunschweig said the state court had wrongly declared it was not responsible for hearing the case which should now go ahead.
He has not 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 her disappearance there in 2007. He has denied any involvement in her disappearance.
Brueckner is currently serving a seven-year prison sentence in Germany for a rape committed in Portugal in 2005.
Earlier this year, German prosecutors said items seized in fresh searches for evidence in the case cannot yet be linked with the investigation.
A large section of the Barragem do Arade reservoir in Portugal was cordoned off in May, about 30 miles from where the three-year-old went missing.
Police flattened a specific area of woodland and dug a number of holes near the remote reservoir as part of a three-day hunt for evidence.
Prosecutor for the city of Braunschweig, Christian Wolters, said the individual items seized as part of searches would be evaluated over the coming days and weeks.
In a short statement, Mr Wolters said the investigation into 46-year-old Brueckner is expected to continue for a long time.
He said the co-operation between German, British and Portuguese authorities went “excellently and very constructively”.
Police were given the go-ahead to search the area after German prosecutors received “certain tips” about the case.
Madeleine vanished while on holiday with her parents in Praia da Luz, after they left her and her younger twin siblings asleep in their apartment while they went out to dinner with friends.