Frankfurt police said a swastika was painted on the cabinet inside the prayer room, which is located in the airport transit area.
Written scrolls containing the Torah, the first five books of the Old Testament, are kept in cabinets knows as arks and removed and read from during Jewish services.
“It is simply sad. This hatred of Jews must finally stop,” Germany's Orthodox Rabbinical Conference said in a statement. “The ugly grimace of antisemitism does not stop even in a highly secured area, at a place of encounter, silence and stopping, where people from all over the world meet briefly while traveling and are in transit.”
Anti-Jewish incidents and attacks in the country have risen in recent years.
According to official figures, police in Germany registered 2,428 antisemitic crimes last year.