Conventional image formats have limited information conveyance, while Hyperspectral Imaging (HSI) offers a broader representation through continuous spectral bands, capturing hundreds of spectral features. However, this abundance leads to redundant information, posing a computational challenge for deep learning models. Thus, models must effectively extract indicative features. HSI’s non-linear nature, influenced by environmental factors, necessitates both linear and non-linear modeling techniques for feature extraction. While PCA and ICA, being linear methods, may overlook complex patterns, Autoencoders (AE) can capture and represent non-linear features. Yet, AEs can be biased by unbalanced datasets, emphasizing majority class features and neglecting minority class characteristics, highlighting the need for careful dataset preparation. To address this, the Dual-Path AE (D-Path-AE) model has been proposed, which enhances non-linear feature acquisition through concurrent encoding pathways. This model also employs a down-sampling strategy to reduce bias towards majority classes. The study compared the efficacy of dimensionality reduction using the Naïve Autoencoder (Naïve AE) and D-Path-AE. Classification capabilities were assessed using Decision Tree, Support Vector Machine, and K-Nearest Neighbors (KNN) classifiers on datasets from Pavia Center, Salinas, and Kennedy Space Center. Results demonstrate that the D-Path-AE outperforms both linear dimensionality reduction models and Naïve AE, achieving an Overall Accuracy of up to 98.31% on the Pavia Center dataset using the KNN classifier, indicating superior classification capabilities.