Sorting seedlings is laborious and requires attention to identify damage. Separating healthy seedlings from damaged or defective seedlings is a critical task in indoor farming systems. However, sorting seedlings manually can be challenging and time-consuming, particularly under complex lighting conditions. Different indoor lighting conditions can affect the visual appearance of the seedlings, making it difficult for human operators to accurately identify and sort the seedlings consistently. Therefore, the objective of this study was to develop a defective-lettuce-seedling-detection system under different indoor cultivation lighting systems using deep learning algorithms to automate the seedling sorting process. The seedling images were captured under different indoor lighting conditions, including white, blue, and red. The detection approach utilized and compared several deep learning algorithms, specifically CenterNet, YOLOv5, YOLOv7, and faster R-CNN to detect defective seedlings in indoor farming environments. The results demonstrated that the mean average precision (mAP) of YOLOv7 (97.2%) was the highest and could accurately detect defective lettuce seedlings compared to CenterNet (82.8%), YOLOv5 (96.5%), and faster R-CNN (88.6%). In terms of detection under different light variables, YOLOv7 also showed the highest detection rate under white and red/blue/white lighting. Overall, the detection of defective lettuce seedlings by YOLOv7 shows great potential for introducing automated seedling-sorting systems and classification under actual indoor farming conditions. Defective-seedling-detection can improve the efficiency of seedling-management operations in indoor farming.