Kosaka Kumiko was also charged with physically abusing the students at the Antonio Provolo Institute for children with hearing impairment in northwestern Mendoza province.
The 42-year-old nun, who was born in Japan but has Argentine citizenship, denied any wrongdoing.
Kumiko lived at the school between 2004 and 2012, according to authorities. She had been on the run for about a month before she turned herself in this week.
A former student accused the nun of forcing her to wear a diaper to conceal bleeding after she was allegedly raped by priest Horacio Corbacho, prompting police to investigate.
Corbacho, fellow priest Nicola Corradi and three other men were arrested last year after they were charged with sexually abusing at least two dozen students at the school.
They are being held at a jail in Mendoza and have not spoken publicly since the arrest. If found guilty, the accused face 10 to 50 years in prison.