A correct food tray sealing is required to preserve food properties and safety for consumers. Traditional food packaging inspections are made by human operators to detect seal defects. Recent advances in the field of food inspection have been related to the use of hyperspectral imaging technology and automated vision-based inspection systems. A deep learning-based approach for food tray sealing fault detection using hyperspectral images is described. Several pixel-based image fusion methods are proposed to obtain 2D images from the 3D hyperspectral image datacube, which feeds the deep learning (DL) algorithms. Instead of considering all spectral bands in region of interest around a contaminated or faulty seal area, only relevant bands are selected using data fusion. These techniques greatly improve the computation time while maintaining a high classification ratio, showing that the fused image contains enough information for checking a food tray sealing state (faulty or normal), avoiding feeding a large image datacube to the DL algorithms. Additionally, the proposed DL algorithms do not require any prior handcraft approach, i.e., no manual tuning of the parameters in the algorithms are required since the training process adjusts the algorithm. The experimental results, validated using an industrial dataset for food trays, along with different deep learning methods, demonstrate the effectiveness of the proposed approach. In the studied dataset, an accuracy of 88.7%, 88.3%, 89.3%, and 90.1% was achieved for Deep Belief Network (DBN), Extreme Learning Machine (ELM), Stacked Auto Encoder (SAE), and Convolutional Neural Network (CNN), respectively.