Objective: To determine the nature, extent, and cost of discrepancies between the quantities of medications supplied to medical departments and administered to patients in public hospitals. Design: Multicentre, retrospective observational study; analysis of electronic pharmacy drug management system (medication supply) and medication administration data for twenty frequently used medications. Setting, participants: Medical, surgical, and emergency department (ED) wards in each of four public hospitals in Melbourne, Victoria, during the 2019 calendar year. Main outcome measures: Discrepancy between the quantity of medication supplied and administered to patients (as proportion of medication supplied), overall and by hospital and ward type; direct cost to the hospitals of the discrepancies. Results: The overall discrepancy rate (all medications, hospitals, ward types) was 19.2% (95% CI, 19.0-19.4%); overall rates by hospital ranged from 5.8% (95% CI, 5.7-5.9%) to 26.7% (95% CI, 26.6-26.9%). The discrepancies were largest for medications useful for self-treatment oral antibiotics (eg, phenoxymethylpenicillin 250 mg capsule, 86.8%; 95% CI, 83.1-89.9%) and gastrointestinal medications (eg, ondansetron 4 mg tablet, 53.3%; 95% CI, 52.953.7%). Discrepancies were larger for oral than equivalent (or similar) parenteral formulations; they were generally low for controlled medications (temazepam, diazepam, oxycodone). Overall discrepancies were larger for EDs (32.3%; 95% CI, 32.2-32.5%) than for admitted patient wards, but differed between EDs (range: 25.7%; 95% CI, 25.5-26.0% to 39.5%; 95% CI, 392-39.7%). The estimated direct cost to hospitals of the discrepancies for the selected medications was $27 800. Conclusion: Substantial quantities of medications supplied to hospital wards and EDs are not accounted for in electronic administration records.