Technologies for rapid identification and prediction of food spoilage can be crucial in minimizing food waste and losses, although their efficiency requires further improvement. This study aimed to pinpoint specific near-infrared (NIR) wavelengths that could indicate spoilage in raw chicken breast fillets. In this study, commercial tray-packs of boneless, skinless chicken breast fillets stored in a walk-in cooler at 4 °C were periodically tested every other day until they reached the spoilage state (identified by > 7 log CFU/ml). A portable Hyper spectral spectroscopy device (Field Spec Hi-Res4), with a range of wavelengths of 350–2500 nm, was used to measure reflectance. In addition to hyper-spectral analysis, aerobic plate counts were conducted on the fillets. The data from these counts were then used to train a Back Propagation Neural Network (B.P.N.N.) with specific parameters (250,000 steps, a learning rate of 0.02, and 5 hidden layers) and Linear-Support Vector machines (SVM-Linear) with ten-fold cross-validation technique to categorize spoilage into three stages: baseline microbial count (up to 3 log CFU/ml) (Initiation), propagation (between 3 and 6.9 log CFU/ml), and spoiled (> 7 log CFU/ml). The feature extraction process successfully identified the most representative signature wavelengths of 385 nm, 400 nm, 432 nm, 1141 nm, 1321 nm, 1374 nm, 2241 nm, 2292 nm, 2311 nm, and 2412 nm from the whole hyper-spectral profile, which facilitated the classification of different phases of spoilage. The BPNN model demonstrated a high classification accuracy, with 93.7% for baseline counts, 95.2% for the propagation phase, and 98% for the spoiled category. These signature hyperspectral wavelengths hold the potential for developing cost-effective and rapid food spoilage detection systems, particularly for perishable items.