The persistence of non-typhoidal Salmonella and Campylobacter in chicken meat is a considerable public health risk and a future challenge. This study aimed to determine the prevalence of Salmonella and Campylobacter in poultry processing lines where different chlorine concentrations were used in the chill tank. The samples were collected from four types of processing plants in Sri Lanka, considering the chlorine concentration used in the chill tank, which ranged from 2 ppm to 50 ppm. Salmonella and Campylobacter were isolated from whole carcass washings, neck skin, and cecal samples. Subsequently, an antimicrobial susceptibility test was performed for the isolates. The results revealed the overall prevalence of Salmonella and Campylobacter was 78.25% and 63.5%, respectively. Positive percentages of Salmonella and Campylobacter were high in the carcasses compared to the neck skin and ceca. The Campylobacter counts on the whole carcasses were significantly low (p < 0.001), at higher chlorine concentrations ranging from 20 to 30 ppm and 40 to 50 ppm. The pathogen prevalence in the whole carcasses was 84.7% Campylobacter coli, 39.1% Campylobacter jejuni, 71.1% Salmonella Typhimurium, and 28.8% Salmonella Infantis. The highest resistance was observed for tetracycline (63.8%) in Salmonella, while it was for gentamicin (87.8%) in Campylobacter. The prevalence percentage of multidrug-resistant Campylobacter was 51.2%, while it was 2.12% for Salmonella. The persistence of multidrug-resistant Salmonella and Campylobacter on the post-chill carcasses was highlighted in the present study as a significant public health threat that has to be addressed urgently.