This paper is considered with joint estimation of state and time-varying noise covariance matrices in non-linear stochastic state space models. We present a variational Bayes and Gaussian filtering based algorithm for efficient computation of the approximate filtering posterior distributions. The Gaussian filtering based formulation of the non-linear state space model computation allows usage of efficient Gaussian integration methods such as unscented transform, cubature integration and Gauss-Hermite integration along with the classical Taylor series approximations. The performance of the algorithm is illustrated in a simulated application.