The human population is growing at a very rapid scale. With this progressive growth, it is extremely important to ensure that healthy food is available for the survival of the inhabitants of this planet. Also, the economy of developing countries is highly dependent on agricultural production. The overall economic balance gets affected if there is a variance in the demand and supply of food or agricultural products. Diseases in plants are a great threat to the yield of the crops thereby causing famines and economy slow down. Our present study focuses on applying machine learning model for classifying tomato disease image dataset to proactively take necessary steps to combat such agricultural crisis. In this work, the dataset is collected from publicly available plant–village dataset. The significant features are extracted from the dataset using the hybrid-principal component analysis–Whale optimization algorithm. Further the extracted data are fed into a deep neural network for classification of tomato diseases. The proposed model is then evaluated with the classical machine learning techniques to establish the superiority in terms of accuracy and loss rate metrics. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.