OBJECTIVE: To examine trends in effective medical treatment coverage for hypertension, diabetes and dyslipidaemia in Japan, using a metric to assess effective coverage of health interventions derived from a health system performance assessment framework. METHODS: We obtained cross-sectional data for 96,863 individuals aged 40-74 years from the 15 annual Japanese National Health and Nutrition Surveys (2003-2017). We defined treatment need for hypertension, diabetes and dyslipidaemia as biomarkers equal to or greater than diagnostic thresholds or medication use. For individuals needing treatment, we conducted nearest-neighbour matching to estimate treatment effects and effective coverage, defined as the fraction of potential reductions in biomarkers actually achieved in treated individuals by medications. RESULTS: The age-standardized prevalence of treatment need for hypertension, diabetes and dyslipidaemia remained around 40%, 7% and 33%, respectively, in 2003-2017. Average treatment effects for those treated in 2013-2017 were 14.8 mmHg (95% confidence interval: 14.2-15.4) for systolic blood pressure, 1.2 percentage points (0.8-1.6) for haemoglobin A1c and 57.9 mg/dl (56.6-59.2) for non-high-density lipoprotein cholesterol. Effective coverage significantly increased between 2003-2007 (hypertension: 48.4% [44.7-52.0], diabetes: 43.8% [35.7-51.8], dyslipidaemia: 86.3% [83.1-89.5]) and 2013-2017 (hypertension: 76.2% [74.2-78.2], diabetes: 74.7% [71.0-78.5], dyslipidaemia: 94.6% [93.3-95.9]). CONCLUSIONS: Effective coverage of medical treatment for metabolic risk factors has increased. Most of the potential reductions in non-high-density lipoprotein cholesterol have been achieved by statins. Further efforts are necessary to improve the effectiveness of antihypertensive and antidiabetic drugs.