Charged lepton system symmetry under combined charge, parity, and time-reversal transformation (CPT) remains scarcely tested. Despite stringent quantum-electrodynamic limits, discrepancies in predictions for the electron–positron bound state (positronium atom) motivate further investigation, including fundamental symmetry tests. While CPT noninvariance effects could be manifested in non-vanishing angular correlations between final-state photons and spin of annihilating positronium, measurements were previously limited by knowledge of the latter. Here, we demonstrate tomographic reconstruction techniques applied to three-photon annihilations of ortho-positronium atoms to estimate their spin polarisation without magnetic field or polarised positronium source. We use a plastic-scintillator-based positron-emission-tomography scanner as a high-acceptance photon detector to study CPT-prohibited angular correlation in ortho-positronium (o-Ps) annihilations. We record an unprecedented range of kinematical configurations of o-Ps annihilations into three photons. Tomographic reconstruction of the annihilation points in a large medium allows single-event estimation of positronium spin orientation and, consequently, determination of the complete spectrum of angular correlation between the annihilation plane orientation and positronium spin, the non-vanishing expectation value of which would manifest CPT-violating effects. We find no violation at the precision level of 10^{−4}, with a fourfold improvement on the previous measurement. This work enables application of positronium-imaging techniques to study discrete symmetries in positronium decays.