A film deposition method includes steps of transferring a substrate having a pattern including a concave part into a vacuum chamber; supplying a first reaction gas to the substrate from a first reaction gas supplying part, thereby allowing the first reaction gas to be adsorbed on the substrate; supplying a second reaction gas that reacts with the first reaction gas to the substrate from a second reaction gas supplying part, thereby allowing the first reaction gas adsorbed on the substrate to react with the second reaction gas and forming a reaction product of the first and the second reaction gases on the substrate; supplying an alteration gas to the substrate through an activated gas supplying part capable of activating the alteration gas; and supplying an etching gas to the substrate chamber through the activated gas supplying part under an environment where the reaction product is not formed.