Workplace violence (WPV) is a major public health concern, especially among healthcare workers. There is a negative perception and poor practice of healthcare employers towards WPV prevention. This study aims to determine the perception and practice towards WPV prevention and its associated factors among healthcare employers in Melaka, Malaysia. A cross-sectional study was conducted by recruiting 162 healthcare employers, using a validated questionnaire and utilised linear regression analysis. The participants had a mean percentage of 67.2% for perception and 80% for practice towards WPV prevention. The perception towards WPV prevention is associated with the following characteristics: female (adjusted ß = −3.95; 95% CI: −7.81, −0.09; p = 0.045), Indian ethnicity (adjusted ß = 16.04; 95% CI: 2.34, 29.74; p = 0.022), other ethnicities (adjusted ß = 25.71; 95% CI: 8.94, 42.47; p = 0.003), degree holder (adjusted ß = 4.35; 95% CI: 0.15, 8.54; p = 0.042), masters holder (adjusted ß = 7.63; 95% CI: 1.11, 14.14; p = 0.022), and enough funds (adjusted ß = −5.46; 95% CI: −9.25, −1.67; p = 0.005). Meanwhile, the practice towards WPV prevention is significantly associated with Chinese ethnicity (adjusted ß = −9.25; 95% CI: −18.36, −0.14; p = 0.047), Indian ethnicity (adjusted ß = −14.97; 95% CI: −29.48, −0.46; p = 0.043), other ethnicities (adjusted ß = 23.55; 95% CI: 5.59, 41.51; p = 0.011), degree holder (adjusted ß = −4.41; 95% CI: −8.67, −0.14; p = 0.043), and availability of standard operating procedure for reporting WPV (adjusted ß = 6.07; 95% CI: 1.58, 10.57; p = 0.008). The high perception and practice towards WPV prevention and its associated factors among healthcare employers provide evidence-based input to improve the existing measures for WPV prevention.