In a vertical substrate processing apparatus including a vertical reaction vessel having an open lower end, a lid closing the open lower end of the reaction vessel, a rotation shaft extending through the lid to rotate a wafer boat in the reaction vessel, a bore formed in a casing disposed below the lid to receive the rotation shaft is sealed hermetically by a magnetic sealing unit, the leakage of a gas emanated from magnetic fluid of the magnetic sealing unit into the reaction vessel is suppressed during a LPCVD process and, if the vertical processing apparatus is used for both a LPCVD process and an oxidation process, the corrosion of the components of a rotating mechanism by HCl gas is prevented. To achieve such functions, the bore is evacuated through an exhaust passage opening in to the bore at a position on the side of the reaction vessel with respect to the magnetic sealing unit. The deposition of reaction byproducts on rotating members can be prevented by supplying an inert gas, such as N.sub.2 gas, through a gas supply passage when the bore is evacuated. When carrying out an oxidation process, a purging gas is supplied through the gas supply passage into the bore to prevent leakage of HCl gas into the bore.