This cohort study aimed to identify the associations of dairy protein intake with the risk of developing a low muscle mass during a 12-year follow-up period, using data from 4412 middle-aged Korean Genome and Epidemiology Study participants with a normal baseline muscle mass. Dairy protein intake at baseline was assessed using a semi-quantitative Food Frequency Questionnaire. Skeletal muscle mass index (SMI), defined as the weight-adjusted skeletal muscle mass, was measured biennially using multi-frequency bioelectrical impedance analyses. Cox proportional hazards regression analysis was used to calculate multivariable-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs). Overall, 395 subjects developed a low SMI (%) during an average follow-up of 141 (19–152) months. The average consumption of milk and other dairy products was 73.6 and 104.1 g/day, respectively. In men, a higher dairy protein intake was associated with a decreased risk of developing a low SMI (tertile 3 [T3] vs. T1, HR: 0.63; 95% CI: 0.42, 0.94; p for trend = 0.029). In a stratified analysis according to a total protein intake, this association was stronger in the lower-protein intake group (HR: 0.59; 95% CI: 0.35, 0.99; p for trend = 0.036) but not detected in the higher-protein intake group. Men who consumed milk ≥1 time/day had a significantly lower risk of developing a low SMI (HR: 0.62; 95% CI: 0.39, 0.98; p for trend = 0.023). No significant associations were observed in women. In summary, dairy consumption appears to be beneficial for decreasing the risk of developing a low muscle mass in middle-aged Korean men.