The investigation into Khodorkovsky was for alleged money laundering, according to a report to be published in Saturday's Süddeutsche Zeitung. The Munich-based paper was unable to say if the probe was still under way.
Khodorkovsky was suspected of having placed between €15 million and €20 million ($20 million to $28 million) in a German bank account in his name and those of close associates, court sources told the newspaper.
Investigators came across Khodorkovsky's name on a CD-ROM containing client data of Swiss private bank Julius Baer, which they obtained after a raid of the bank's offices in Frankfurt, southern Germany.
A Russian court jailed the fallen oil tycoon in 2005 for the theft of Russian oil and money laundering in a trial his supporters insist was part of a political campaign against him.
Last month, the European Court of Human Rights ruled that Yukos had not received a fair trial but cleared the Russian government of having mounted a politically motivated campaign against the company.