The winger, who plays for French club Reims, is under investigation by Japanese police over the alleged incident in Osaka last year. He denies any wrongdoing.
"Junya Ito filed a suit seeking 200 million yen in compensation for damages against the two women," said lawyer Hirotaro Kato, who is representing Ito.
"It is extremely important to restore his honour as soon as possible, as a period of a player's career is limited," Kato told reporters on Monday.
Local media reports said Ito's physical trainer has also been accused.
A report about the accusations against Ito was published in a Japanese magazine while the player was at the Asian Cup in Qatar last month.
He left the Japan squad before their quarter-final against Iran, with the Japan Football Association saying they wanted to protect the team from "noise" and "provide an environment where they can concentrate on football".
Ito has played twice for Reims after returning to his club.
Reims have expressed "support for its player ... awaiting concrete elements which will shed light on the alleged facts and (the club) will follow with great attention the related legal progress".
Ito has played 54 games for Japan, scoring 13 goals.
