Mycobacterium avium subsp. paratuberculosis (MAP) in milk of bovine origin is suspected of being implicated in Crohn's disease in humans. Milk can be contaminated via direct excretion of MAP in milk or indirectly via fecal contamination of the milk. This study aimed at estimating the level of MAP in farm bulk tank milk and simulating the effect of direct and indirect contamination with MAP. The effect of discarding milk from test-positive cows at different prevalences was assessed. The concentration of MAP in milk was estimated using a simulation model, while taking direct and indirect contamination with MAP into account. Direct MAP contamination of milk was related to infection stages, while indirect contamination was associated with within-herd prevalence and distribution of cows in different stages of infection. Discarding of milk based on diagnostic test results was included as a control option. Median MAP load in farm bulk tank milk at within-herd infection prevalences from 7.5% to 60% were estimated to be 0.54-7.53 CFU/mL milk. Maximum concentration at the prevalence of 60% could be 1186 CFU/mL caused by shedding of high amounts of MAP in feces. At the prevalence of 15%, discarding milk from test positive cows would result in discarding 11% of milk and reduce the MAP level by 80%. Due to poor sensitivity of the diagnostic test, removing test-positive cows would not further reduce the already low concentration of MAP and it would not guarantee the milk as MAP-free. The model was relatively simple yet capable of capturing true infection status and associated contributions from milk and feces. Further knowledge on distribution of fecal excretion from infected cows is required because very few "super-shedders" might play a major role.