Heim, born in Austria 91 years ago, is accused of torturing and killing hundreds of prisoners at the Mauthausen concentration camp in Austria in 1941 and 1942, the New York Times reported.
His alleged crimes include injecting gasoline into the hearts of victims, conducting operations on prisoners without anesthesia and executing prisoners just to record how long they took to die.
Spanish police began searching for Heim over the summer after the German government detected large transfers of money to Spain from Heim's family in Germany.
Heim has been a fugitive since 1962, when he fled his home in Baden-Baden, Germany.
In 1979, a Berlin court declared him a major Nazi war criminal and convicted him in absentia of killing scores of prisoners at the Mauthausen concentration camp.