Preserving the privacy and security of big data in the context of cloud computing, while maintaining a certain level of efficiency of its processing remains to be a subject, open for improvement. One of the most popular applications epitomizing said concerns is found to be useful in genome analysis. This work proposes a secure multi-label tumor classification method using homomorphic encryption, whereby two different machine learning algorithms, SVM and XGBoost, are used to classify the encrypted genome data of different tumor types.