Recently it was shown that the topological properties of $2D$ and $3D$ topological insulators are captured by a $Z_2$ chiral anomaly in the boundary field theory. It remained, however, unclear whether the anomaly survives elctron-electron interactions. We show that this is indeed the case, thereby providing an alternative formalism for treating topological insulators in the interacting regime. We apply this formalism to fractional topological insulators (FTI) via projective/parton constructions and use it to test the robustness of all fractional topological insulators which can be described in this way. The stability criterion we develop is easy to check and based on the pairswitching behaviour of the noninteracting partons. In particular, we find that FTIs based on bosonic Laughlin states and the $M=0$ bosonic Read-Rezayi states are fragile and may have a completely gapped and non-degenerate edge spectrum in each topological sector. In contrast, the $Z_{k}$ Read-Rezayi states with $M=1$ and odd $k$ and the bosonic $3D$ topological insulator with a $\pi/4$ fractional theta-term are topologically stable.