The 63-year-old Katsav, who resigned the presidency in 2007, was also indicted on a charge of obstruction of justice and witness tampering in one of the cases, Attorney General Menachem Mazuz said.
The alleged crimes could bring decades of prison time for Katsav if he is convicted, The Jerusalem Post reported.
The indictment returned at Tel Aviv District Court accuses Katsav of twice raping and engaging in a "forceful indecent act" against a female staffer while he was tourism minister in 1996-1999.
It also includes two counts of sexual harassment against two other women in the president's residence, the Post said.
The prosecution named 56 witnesses, including the alleged victims, identified only by letters of the alphabet, and numerous public figures.
The witness list also includes six other women expected to testify about similar acts for which the statute of limitations expired for criminal prosecution, the Post said.
The most serious allegations concern a woman known as Tourism Ministry Aleph, whom prosecutors argue Katsav raped on two separate occasions.
Katsav rejected a plea bargain in 2008 that would have let him avoid rape charges in exchange for admitting to lesser sexual offenses.
Katsav denies wrongdoing and says he's a victim of a political and media-driven witch-hunt. His lawyer Amnon Shomron said the indictment had no evidence to back it up.