An apparatus for transporting a substrate includes a base, a holding device which retracts relative to the base and holds multiple substrates in multiple stages, respectively, a detection device including three detection components such that the three detection components are positioned to detect peripheries of the substrates held by the holding device from different positions, respectively, and a control device including circuitry which estimates a position of the substrates based on detection result of the detection device, calculates an amount of shifting between a base position and an estimated position of the substrates, determines whether a calculated amount of shifting is within a threshold value, and executes transport of the substrates held by the holding device when the calculated amount of shifting is determined to be within the threshold value.