The invention provides a vehicle control system, a vehicle control method, and a vehicle control program. A vehicle control system includes: an automated driving control part that performs automated driving in which at least one of acceleration/deceleration and steering of a vehicle is automatically controlled; a driving operation element that receives an operation of an occupant with respect to acceleration/deceleration and steering of the vehicle; an operation element state change part that makes the driving operation element disabled when the automated driving by the automated driving control part is performed; and an alternative operation reception part that receives an operation which is different from the operation with respect to the driving operation element by the occupant when the driving operation element is disabled by the operation element state change part, wherein the automated driving control part controls at least one of acceleration/deceleration and steering of the vehicle based on the operation by the alternative operation reception part.