Flows with velocity profiles very different from the parabolic velocity profile can occur in the entrance region of a tube as well as in tubes with converging/diverging cross-sections. In this paper, asymptotic and numerical studies are undertaken to analyse the temporal stability of such ‘non-parabolic’ flows in a flexible tube in the limit of high Reynolds numbers. Two specific cases are considered: (i) developing flow in a flexible tube; (ii) flow in a slightly converging flexible tube. Though the mean velocity profile contains both axial and radial components, the flow is assumed to be locally parallel in the stability analysis. The fluid is Newtonian and incompressible, while the flexible wall is modelled as a viscoelastic solid. A high Reynolds number asymptotic analysis shows that the non-parabolic velocity profiles can become unstable in the inviscid limit. This inviscid instability is qualitatively different from that observed in previous studies on the stability of parabolic flow in a flexible tube, and from the instability of developing flow in a rigid tube. The results of the asymptotic analysis are extended numerically to the moderate Reynolds number regime. The numerical results reveal that the developing flow could be unstable at much lower Reynolds numbers than the parabolic flow, and hence this instability can be important in destabilizing the fluid flow through flexible tubes at moderate and high Reynolds number. For flow in a slightly converging tube, even small deviations from the parabolic profile are found to be sufficient for the present instability mechanism to be operative. The dominant non-parallel effects are incorporated using an asymptotic analysis, and this indicates that non-parallel effects do not significantly affect the neutral stability curves. The viscosity of the wall medium is found to have a stabilizing effect on this instability.