Some plant diseases can significantly reduce harvest, but their early detection in cultivation may prevent those consequential losses. Conventional methods of diagnosing plant diseases are based on visual observation of crops, but the symptoms of various diseases may be similar. It increases the difficulty of this task even for an experienced farmer and requires detailed examination based on invasive methods conducted in laboratory settings by qualified personnel. Therefore, modern agronomy requires the development of non-destructive crop diagnosis methods to accelerate the process of detecting plant infections with various pathogens. This research pathway is followed in this paper, and an approach for classifying selectedSolanum lycopersicumdiseases (anthracnose, bacterial speck, early blight, late blight and septoria leaf) from hyperspectral data captured on consecutive days post inoculation (DPI) is presented. The objective of that approach was to develop a technique for detecting infection in less than seven days after inoculation. The dataset used in this study included hyperspectral measurements of plants of two cultivars ofS. lycopersicum: Benito and Polfast, which were infected with five different pathogens. Hyperspectral reflectance measurements were performed using a high-spectral-resolution field spectroradiometer (350–2500 nm range) and they were acquired for 63 days after inoculation, with particular emphasis put on the first 17 day-by-day measurements. Due to a significant data imbalance and low representation of measurements on some days, the collective datasets were elaborated by combining measurements from several days. The experimental results showed that machine learning techniques can offer accurate classification, and they indicated the practical utility of our approaches.