The crimes are alleged to have been committed in facilities run by a Roman Catholic order that operates more than 250 hospitals around the world.
“The charge relates to the sexual abuse of four patients in the care of institutions run by the Hospitaller Order of Saint John of God,” prosecutors said in a statement on Thursday.
According to the indictment, the alleged acts were committed in 2004, 2005 and 2010 in several hospitals run by the religious order, one of which was a hospital for the mentally ill.
The Portuguese courts opened an investigation in December 2012 after several reports of sexual abuse of the mentally ill, including a child, in institutions run by the Order of Hospitallers.
The Portuguese Catholic Church was already under fire at that time due to the case of a priest named Luis Miguel Mendes, former vice-rector of the Fundao Seminary, who was sentenced in 2013 to 10 years in prison for the sexual abuse of six minors aged between 13 and 15.