To investigate differences in the prevalence of specific chronic diseases in Australia by selected measures of socio-economic position, and by age group and sex, using representative national census population data. Cross-sectional, whole of population study; analysis of 2021 Australian census data. People aged 40 years or older for whom 2021 Australian census health status and socio-economic position-related data were available. Age-standardised prevalence of ten chronic diseases (arthritis, asthma, cancer, dementia, diabetes, heart disease, kidney disease, lung disease, mental health conditions, and stroke), by socio-economic position (Index of Relative Socio-economic Disadvantage [IRSD], income category, educational level, occupational grade), age group, and sex; mean change in prevalence across socio-economic position categories. Health status responses and data that allowed IRSD categorisation were available for 11.3 million people aged 40 years or older (92% of all adults aged 40 years or older). The proportions of people who reported nine chronic diseases (exception: cancer) increased with increasing socio-economic disadvantage as measured by IRSD decile and income. The increases were less marked for people aged 80 years or older than for those aged 40-79 years, and more marked for women than men. For people aged 40-59 or 60-79 years, the increase in age-standardised chronic disease prevalence per one decile decrease in IRSD was greatest for lung disease in both women (40-59 years, 18.4% per decile; 60-79 years, 10.6% per decile) and men (40-59 years, 16.9% per decile; 60-79 years, 11.0% per decile). In people aged 80 years or older, the increase in prevalence per one decile decrease in IRSD was greatest for kidney disease in women (6.0% per decile) and for mental health conditions in men (7.1% per decile). The age-standardised prevalence of cancer decreased by 0.4-1.1% per one decile decrease in IRSD for all age groups and both sexes, except for men aged 40-59 years (increased by 0.1% per IRSD decile). Consistent relationships with educational level or occupational grade were not found. The prevalence of chronic disease differs by socio-economic position, but the direction, magnitude, and consistency of the effect differs by disease, socio-economic position measure, age, and sex. Understanding the relationship between different socio-economic position measures and chronic diseases facilitates the formulation of directed interventions.