Anyway, I'm not quite sure if what I think is the same as you, when you say using FT, did you actually transform the field aperture profile only? Such FT relation only holds within the far-field region in which the inequality ##z>>2D^2/\lambda## must be true.
If that's not sufficiently fulfilled, then your experimental conditions might still be in the paraxial/Fresnel region, in which case the FT relation should be performed w.r.t. the aperture profile multiplied by a quadratic phase in the aperture plane ##\exp{\frac{jk}{2z}(\eta^2+\zeta^2)}##. That is, what must be transformed is not only the aperture profile, but there is an additional phase factor. In either case, knowledge of wavelength is necessary.