According to fire brigade reports, the blaze was centred under a wooden ladder that leads to the library.
Firefighters immediately rushed to the scene and extinguished the fire before it threatened the temple and the adjoining library, which features roughly 1,600 rare books and manuscripts.
Authorities in the Cretan port city said the synagogue's main doors were locked and that the alarm system sounded when firefighters broke down the main gate to enter the building.
However, a full investigation is underway to determine the exact cause of the incident.
The medieval synagogue in Hania's old quarter is amongst the most noted Jewish temples in Greece, functioning as both a cultural centre and a house of worship.