The dramatic growth in machine learning has brought in significant features and quantified non‐linear associations in the data derived from sensitive medical datasets. The data should be preserved without influencing the associated classifications by applying a robust, effective and reliable data perturbation technique before enforcing ensemble classification. In this paper, an Integrated Condensation Scheme imposed Privacy Preserving Rotation‐based Data Perturbation and Ensemble Classification (ICS‐PPR‐DPEC) is proposed for ensuring privacy of such sensitive data. Condensation Algorithm‐based Data Perturbation is used for constructing homogenous groups determined from the distance between tuples. It also generates a rotation matrix for conducting perturbation that ensures higher data sensitivity protection before it is sent for classification. Advanced Extreme Learning Machine‐based Ensemble Classification Scheme includes kernel, norm‐optimized and regularized Extreme Learning Machine (ELM)‐based classifiers for attaining predominant classification accuracy in identifying human DNA sequences. This approach facilitates classification by constructing ensembles which are trained through randomly resampled ELM classifiers. It includes an objective function that systematically improves the accuracy and diversity among resulting ensembles. The experimental results of the proposed ICS‐PPR‐DPEC are found to be excellent in terms of classification Accuracy, Precision, Recall, and Kappa statistic when compared to the benchmarked techniques.