Bayesian inference and uncertainty quantification in a general class of non-linear inverse regression models is considered. Analytic conditions on the regression model $\{\mathscr G(θ): θ\in Θ\}$ and on Gaussian process priors for $θ$ are provided such that semi-parametrically efficient inference is possible for a large class of linear functionals of $θ$. A general semi-parametric Bernstein-von Mises theorem is proved that shows that the (non-Gaussian) posterior distributions are approximated by certain Gaussian measures centred at the posterior mean. As a consequence posterior-based credible sets are valid and optimal from a frequentist point of view. The theory is illustrated with two applications with PDEs that arise in non-linear tomography problems: an elliptic inverse problem for a Schrödinger equation, and inversion of non-Abelian X-ray transforms. New analytical techniques are deployed to show that the relevant Fisher information operators are invertible between suitable function spaces