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We describe a perturbation method that can be used to compute the multivariate generating function (MGF) of a non-simple polyhedron, and then construct a perturbation that works for any transportation polytope. Applying this perturbation to the family of central transportation polytopes of order $kn \times n$, we obtain formulas for the MGF of the polytope. The formulas we obtain are enumerated by combinatorial objects. A special case of the formulas recovers the results on Birkhoff polytopes given by the author and De Loera and Yoshida. We also recover the formula for the number of maximum vertices of transportation polytopes of order $kn \times n$.