Arnold Pier, who until recently was head doctor at the clinic, has been charged with three counts of causing bodily harm leading to death and four counts of manslaughter, prosecutors in Mönchengladbach said in a statement.
Police issued last week a warrant for the arrest of the 52-year-old surgeon, whose was provisionally struck off the medical register last year, after fears that he might flee. Eight other doctors - including three still working at the clinic in Wegberg, in western Germany - were charged with giving incorrect treatment, including in cases where patients died.
According to news media reports, Pier gave incorrect diagnoses and carried out operations such as removing patients' appendices or gall bladders unnecessarily and using lemon juice as a disinfectant.
Westdeutscher Rundfunk radio cited Pier's lawyer as saying the charges were part of an "unprecedented attempt at character assassination" by "a group of interested parties" aimed at destroying his reputation and driving him out of the clinic.