A tolerance error estimating apparatus, method, program, reconstruction apparatus and control apparatus capable of estimating a deviation of a drive axis from a reference position with respect to driving time are provided. A tolerance error estimating apparatus (processing apparatus 300) X-ray analysis apparatus comprises a specific position calculating section 320 for obtaining a specific position of a reference sample at each rotation driving time from X-ray detection images and a deviation amount calculating section 330 for calculating the deviation amount Δx in the x direction and Δy in the y direction of the center position of a rotation drive shaft as the rotation drive axis at each rotation driving time from the reference position based on the specific position, when the z direction of the orthogonal coordinate system fixed to the sample is set the direction parallel to the rotation drive axis.