Both the DFB premises and those of the German Football League (DFL) were raided on Tuesday afternoon after a search warrant was issued by the district court in Bonn.
Documents were seized by plain-clothed police and officers from the Federal Cartel Office (FCO) - which protects against monopolies - amidst suspicion of "competition-limiting arrangements".
"We have taken legal advice," DFB general secretary Wolfgang Niersbach told German sports agency SID.
"We want to exhaust all judicial means to defend ourselves against this approach."
The DFB are unhappy about the heavy-handed tactics, insisting they would have complied with any requests for information or documents, and have submitted a formal complaint to the authorities.
"We are accountable to our six million members," said Niersbach.
The FCO in Bonn rejected the criticism and said the matter will be decided by the district court in Bonn, who granted the search warrant of the DFB and DFL premises.
"In case of a complaint about the search into the DFB and DFL offices, the matter will be argued with the district court who decided to give us a search warrant," said FCO spokeswoman Silke Kaul.