Background Overweight and obesity impose a significant health burden in Australia, predominantly the middle-aged and older adults. Studies of the association between obesity and chronic diseases are primarily based on cross-sectional data, which is insufficient to deduce a temporal relationship. Using nationally representative panel data, this study aims to investigate whether obesity is a significant risk factor for type 2 diabetes, heart diseases, asthma, arthritis, and depression in Australian middle-aged and older adults. Methods Longitudinal data comprising three waves (waves 9, 13 and 17) of the Household, Income and Labour Dynamics in Australia (HILDA) survey were used in this study. This study fitted longitudinal random-effect logistic regression models to estimate the between-person differences in the association between obesity and chronic diseases. Results The findings indicated that obesity was associated with a higher prevalence of chronic diseases among Australian middle-aged and older adults. Obese adults (Body Mass Index [BMI] [greater than or equal to] 30) were at 12.76, 2.05, 1.97, 2.25, and 1.96, times of higher risks of having type 2 diabetes (OR: 12.76, CI 95%: 8.88-18.36), heart disease (OR: 2.05, CI 95%: 1.54-2.74), asthma (OR: 1.97, CI 95%: 1.49-2.62), arthritis (OR: 2.25, 95% CI: 1.90-2.68) and depression (OR: 1.96, CI 95%: 1.56-2.48), respectively, compared with healthy weight counterparts. However, the study did not find any evidence of a statistically significant association between obesity and cancer. Besides, gender stratified regression results showed that obesity is associated with a higher likelihood of asthma (OR: 2.64, 95% CI: 1.84-3.80) among female adults, but not in the case of male adults. Conclusion Excessive weight is strongly associated with a higher incidence of chronic disease in Australian middle-aged and older adults. This finding has clear public health implications. Health promotion programs and strategies would be helpful to meet the challenge of excessive weight gain and thus contribute to the prevention of chronic diseases.