Seisenbacher, 56, won Olympic middleweight gold in Los Angeles in 1984 and in Seoul in 1988 he became the first judoka to successfully defend his title.
Nina Bussek, a spokeswoman for public prosecutors in Vienna, said that both girls Seisenbacher is alleged to have abused "weren't even 14".
One of them he is accused of abusing over several years from 1998 to 2001, starting when she was 11. He also allegedly attempted to abuse a third girl but she fought him off.
Seisenbacher remains Austria's most successful athlete in the summer Olympics. Since retiring a month after the Seoul Olympics he coached in Austria, Georgia and Azerbaijan.
His lawyer, Bernhard Lehofer, told the Austria Press Agency that "Mr Seisenbacher is aware" of the charges but will not comment on them as "we won't start a media circus".
Prosecutors began investigating in 2013 after his two alleged victims, now adults, came forward.