Metamorphic testing is a valuable approach to verifying machine learning programs where traditional oracles are unavailable or difficult to apply. This paper proposes a technique to prioritize metamorphic relations (MRs) in metamorphic testing for machine learning and deep learning systems, aiming to enhance early fault detection. We introduce five metrics based on diversity in source and follow-up test cases to prioritize MRs. The effectiveness of our proposed prioritization methods is evaluated on three machine learning and one deep learning algorithm implementation. We compare our approach against random-based, fault-based, and neuron activation coverage-based MR ordering. The results show that our data diversity-based prioritization performs comparably to fault-based prioritization, reducing fault detection time by up to 62% compared to random MR execution. Our proposed metrics outperformed neuron activation coverage-based prioritization, providing 5–550% higher fault detection effectiveness. Overall, our approach to prioritizing metamorphic relations leads to increased fault detection effectiveness and reduced average fault detection time. This improvement in efficiency can result in significant time and cost savings when applying metamorphic testing to machine learning and deep learning systems.