Improving diesel engine efficiency and emission reduction have been critical research topics. Recent government regulations have shifted this focus to another important area related to engine health and performance monitoring. Although the advancements in the use of deep learning methods for system monitoring have shown promising results in this direction, designing efficient methods suitable for field systems remains an open research challenge. The objective of this study is to develop a computationally efficient neural network-based approach for identifying unknown parameters of a mean value diesel engine model to facilitate physics-based health monitoring and maintenance forecasting. We propose a hybrid method combining physics informed neural networks, PINNs, and a deep neural operator, DeepONet to predict unknown parameters and gas flow dynamics in a diesel engine. The operator network predicts independent actuator dynamics learnt through offline training, thereby reducing the PINNs online computational cost. To address PINNs need for retraining with changing input scenarios, we propose two transfer learning (TL) strategies. The first strategy involves multi-stage transfer learning for parameter identification. While this method is computationally efficient as compared to online PINN training, improvements are required to meet field requirements. The second TL strategy focuses solely on training the output weights and biases of a subset of multi-head networks pretrained on a larger dataset, substantially reducing computation time during online prediction. We also evaluate our model for epistemic and aleatoric uncertainty by incorporating dropout in pretrained networks and Gaussian noise in the training dataset. This strategy offers a tailored, computationally inexpensive, and physics-based approach for parameter identification in diesel engine sub systems.