Background The occurrence of livestock-associated (LA) MRSA (ST398) in pig herds has emerged as a threat to occupational safety in many parts of the world. Recently, an outbreak of skin lesions due to MRSA occurred in workers at a pig farm in regional Australia and both the humans and pigs were shown to have a high prevalence of carriage of either the human-strain ST93 or porcine strain ST398. This study closely scrutinises this outbreak to determine factors associated with MRSA carriage amongst the workers. Methods Information on potential risk factors was collected from employees by means of a questionnaire. The carriage status of MRSA by workers was assessed by nasal swabs processed using standard laboratory techniques with confirmed isolates subjected to sequence typing. Associations between MRSA carriage in workers and their questionnaire responses were investigated using univariable and multivariable logistic regression. Results Nasal carriage of MRSA was identified in 60% (31/52) of participants. Workers having contact with pigs had 24 times the odds of MRSA carriage compared to workers with no direct contact (OR 23.6; CI 5.2–172.8). In addition, the probability of MRSA carriage in workers was significantly (P < 0.001) associated with the number of hours in contact with pigs and each hour of contact-time per day increased the risk of MRSA carriage by 1.44 times (CI 1.14–1.96). These associations were significant (P < 0.001) for both strains, ST398 and ST93, present on this farm. Using a multivariable logistic regression model that incorporated human exposure to five different pig age groups (dry sows, farrowing, weaner, grower, and finisher) as fixed effects, a significant (P = 0.027) increased odds of MRSA carriage was found for persons working with farrowing sows compared with those who did not (OR 6.39, CI 1.23–39.36). Conclusions This study shows that workers in close contact with pigs on a pig farm where MRSA is present had a higher risk of MRSA carriage as the number of hours of direct contact with pigs increased. Since we have detected a significant association for the human-derived CA-MRSA ST93, similar to the pig-adapted LA-MRSA ST398, we consider ST93 as a potential occupational risk for piggery workers. The risk of MRSA carriage is greatest when working with the farrowing group; therefore, an emphasis is required on personal protective equipment while working in the farrowing house. The study has ramifications for the conduct of surveillance for MRSA in people exposed to pigs.