NIDSs identify malicious activities by analyzing network traffic. NIDSs are trained with the samples of benign and intrusive network traffic. Training samples belong to either majority or minority classes depending upon the number of available instances. Majority classes consist of abundant samples for the normal traffic as well as for recurrent intrusions. Whereas, minority classes include fewer samples for unknown events or infrequent intrusions. NIDSs trained on such imbalanced data tend to give biased predictions against minority attack classes, causing undetected or misclassified intrusions. Past research works handled this class imbalance problem using data-level approaches that either increase minority class samples or decrease majority class samples in the training data set. Although these data-level balancing approaches indirectly improve the performance of NIDSs, they do not address the underlying issue in NIDSs i.e. they are unable to identify attacks having limited training data only. This paper proposes an algorithm-level approach called I-SiamIDS, which is a two-layer ensemble for handling class imbalance problem. I-SiamIDS identifies both majority and minority classes at the algorithm-level without using any data-level balancing techniques. The first layer of I-SiamIDS uses an ensemble of b-XGBoost, Siamese-NN and DNN for hierarchical filtration of input samples to identify attacks. These attacks are then sent to the second layer of I-SiamIDS for classification into different attack classes using m-XGBoost. As compared to its counterparts, I-SiamIDS showed significant improvement in terms of Accuracy, Recall, Precision, F1-score and values of AUC for both NSL-KDD and CIDDS-001 datasets. To further strengthen the results, computational cost analysis was also performed to study the acceptability of the proposed I-SiamIDS.