The influence of manufacturing tolerances on the cogging torque waveforms, as well as the back-EMF waveforms, in 3- and 5-phase flux-switching permanent magnet (FSPM) machines having different numbers of stator/rotor poles is investigated by finite element analyses and experiments. The cause of excessive cogging torque in the prototype FSPM machines has been identified. It is due to modular stator structure which makes it mechanically weak, leading to the intrusion of C-core into the airgap and an uneven inner stator bore. The analyses presented in the paper should be useful to the design and analysis of modular PM machines in general.