A substrate processing apparatus includes a substrate processing unit for performing a process on substrates; a recipe protection unit for prohibiting processing conditions for the process from being changed while the process is being performed on a specific number of substrates; a protection cancellation unit for canceling a prohibition of a change in the process to allow the processing conditions to be changed while the process is being performed on the specific number of substrates; and a modifying unit for modifying the processing conditions. Further, a method for examining substrate processing conditions includes a protection cancellation step of canceling a prohibition of a change in the process to allow the processing conditions to be changed while the process is being performed on the specific number of substrates; and a modifying step of modifying the processing conditions.