Former Nazi and cult leader Paul Schaefer has been charged with the 1976 disappearance of an opponent of former Chilean dictator Gen Augusto Pinochet.
Photographer and left-wing activist Juan Maino was arrested and taken to Mr. Schaefer's secret commune, Colonia Dignidad, and never re-appeared.
Mr. Schaefer was also questioned over the allegation he abused 26 children.
The German, 83, who was deported to Chile from Argentina, already faces charges over another disappearance.
Both Juan Maino and Alvaro Vallejos were last seen at Mr. Schaefer's secluded compound after being arrested by Gen Pinochet's security forces.
Chilean prosecutors and human rights activists have long asserted that Gen Pinochet's military government used Colonia Dignidad as a centre for interrogation and torture.
"Schaefer's arrest was very important," said prosecutor Sergio Concha, representing Mr. Maino's family.
"We knew about the link between Colonia Dignidad and Juan Maino's disappearance, but now that he is available for the judge to interrogate, we can prosecute."
Chile's most wanted fugitive, Mr. Schaefer was a corporal in the German army during World War II before running a religious commune in Chile.
He established the commune south of the Chilean capital, Santiago, after fleeing child abuse allegations in Germany in 1961.