Convolutional neural networks trained using manually generated labels are commonly used for semantic or instance segmentation. In precision agriculture, automated flower detection methods use supervised models and post-processing techniques that may not perform consistently as the appearance of the flowers and the data acquisition conditions vary. We propose a self-supervised learning strategy to enhance the sensitivity of segmentation models to different flower species using automatically generated pseudo-labels. We employ a data augmentation and refinement approach to improve the accuracy of the model predictions. The augmented semantic predictions are then converted to panoptic pseudo-labels to iteratively train a multi-task model. The self-supervised model predictions can be refined with existing post-processing approaches to further improve their accuracy. An evaluation on a multi-species fruit tree flower dataset demonstrates that our method outperforms state-of-the-art models without computationally expensive post-processing steps, providing a new baseline for flower detection applications.