It seems there is a bug with the axes argument in the scipy.fftpack.fft2 function. It does not do what it is supose to do. In [1]: import scipy.fftpack In [2]: import numpy In [3]: x = ones((4,4,2)) In [4]: fx = scipy.fftpack.fft2(x,shape=(8,8),axes = (-3,-2)) In [5]: fx.shape Out[5]: (4, 8, 8) but it is working fine with numpy.dft.fft2 In [1]: import numpy In [2]: x = numpy.ones((4,4,2)) In [3]: fx = numpy.dft.fft2(x,s=(8,8),axes=(-3,-2)) In [4]: fx.shape Out[4]: (8, 8, 2)