We describe the fully gauge invariant cosmological perturbation equations in teleparallel gravity by using the gauge covariant version of the Stewart lemma for obtaining the variations in tetrad perturbations. In teleparallel theory, perturbations are the result of small fluctuations in the tetrad field. The tetrad transforms as a vector in both its holonomic and anholonomic indices. As a result, in the gauge invariant formalism, physical degrees of freedom are those combinations of perturbation parameters which remain invariant under a diffeomorphism in the coordinate frame, followed by an arbitrary rotation of the local inertial (Lorentz) frame. We derive these gauge invariant perturbation potentials for scalar perturbations and present the gauge invariant field equations governing their evolution.