The casino, MV Royale Floatel, is stationed near Dr Salim Ali Bird Sanctuary located between Chorao Island and Ribander village.
GCZMA notice asked why the ship should not be asked to move out from the area which has been marked as CRZ.
Social activist Kashinath Shetye had earlier filed a complaint with GCZMA alleging violation of CRZ rules by the ship.
"The GCZMA officials during the site inspection noted that the vessel is operational without CRZ clearance and hence the authority decided to issue a show-cause notice seeking their reply," a senior official of GCZMA told reporters.