Training a machine learning model over an encrypted dataset is an existing promising approach to address the privacy-preserving machine learning task, however, it is extremely challenging to efficiently train a deep neural network (DNN) model over encrypted data for two reasons: first, it requires large-scale computation over huge datasets; second, the existing solutions for computation over encrypted data, such as homomorphic encryption, is inefficient. Further, for an enhanced performance of a DNN model, we also need to use huge training datasets composed of data from multiple data sources that may not have pre-established trust relationships among each other. We propose a novel framework, NN-EMD, to train DNN over multiple encrypted datasets collected from multiple sources. Toward this, we propose a set of secure computation protocols using hybrid functional encryption schemes. We evaluate our framework for performance with regards to the training time and model accuracy on the MNIST datasets. Compared to other existing frameworks, our proposed NN-EMD framework can significantly reduce the training time, while providing comparable model accuracy and privacy guarantees as well as supporting multiple data sources. Furthermore, the depth and complexity of neural networks do not affect the training time despite introducing a privacy-preserving NN-EMD setting.