The basics of house searches are regulated in federal law. Criminal law itself is federal only (i.e. everything that is a crime in Bavaria is also one in Berlin). In a criminal investigation any German judge can order a search wherever they seem fit. The police responsible for that place is then required to execute the search. The details of the search are regulated in state law which the police then follows.

I can't think of a relevant legal discrepancy that may exist between the laws for ordering searches (there are very tight rules set by the Federal Constitutional Court) but I presume the judge has to take into account the laws where the search takes place. On the other hand my knowledge on criminal investigation law is very rusty.