The premises in the states of Lower Saxony and Thuringia were searched on Thursday morning, the prosecutors' office in the city of Goettingen and the federal crime office said in a joint statement.
A significant amount of evidence was seized and is being analysed, it added, although it declined to name the doctor concerned.
"The operation was initiated because of findings by the federal crime office and the Spanish authorities in connection with the investigations into the Spanish doctor and suspected supplier of illegal drugs, Eufemiano Fuentes," the statement said.
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"As part of the investigations, the suspicion was raised that the (German doctor) was one of the suppliers of illegal drugs to Fuentes," it added.
No further information was available at this time and the investigation was continuing.
The Spanish investigation came to light when the Civil Guard raided addresses in Madrid and Zaragoza in May and found large quantities of anabolic steroids, equipment used for blood transfusions and more than 100 bags of frozen blood.
Fuentes has said he treated athletes, footballers and tennis players as well as cyclists.
Tour de France favourites Jan Ullrich, Ivan Basso and Francisco Mancebo were among nine riders withdrawn on the eve of the race after being included on a list of over 50 professional cyclists involved in the probe.
The International Association of Athletics Federations (IAAF) and the International Tennis Federation (ITF) said last month no track and field athletes or tennis players were implicated.
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