Multireference (MR) diagnostics are common tools for identifying strongly correlated electronic structure that makes single-reference (SR) methods (e.g., density functional theory or DFT) insufficient for accurate property prediction. However, MR diagnostics typically require computationally demanding correlated wave function theory (WFT) calculations, and diagnostics often disagree or fail to predict MR effects on properties. To overcome these challenges, we introduce a semi-supervised machine learning (ML) approach with virtual adversarial training (VAT) of an MR classifier using 15 WFT and DFT MR diagnostics as inputs. In semi-supervised learning, only the most extreme SR or MR points are labeled, and the remaining point labels are learned. The resulting VAT model outperforms the alternatives, as quantified by the distinct property distributions of SR- and MR-classified molecules. To reduce the cost of generating inputs to the VAT model, we leverage the VAT model’s robustness to noisy inputs by replacing WFT MR diagnostics with regression predictions in an MR decision engine workflow that preserves excellent performance. We demonstrate the transferability of our approach to larger molecules and those with distinct chemical composition from the training set. This MR decision engine demonstrates promise as a low-cost, high-accuracy approach to the automatic detection of strong correlation for predictive high-throughput screening.