A method for operating a substrate processing apparatus is provided which can contain generation of particles by generating plasma in a stable manner. After a substrate is disposed in an evacuated vacuum chamber, a rare gas is initially supplied into the vacuum chamber, a voltage is applied to a plasma generating means, and plasma of the rare gas is generated. Subsequently, a reaction gas is supplied into the vacuum chamber, the reaction gas is brought into contact with the plasma of the rare gas, and plasma of the reaction gas is generated. The plasma of the reaction gas is brought into contact with the substrate; and the substrate is processed. Plasma is stably generated not by turning the reaction gas into plasma but by first turning the rare gas into plasma by the plasma generating means, and generation of particles is subsequently suppressed.