Homomorphic encryption enables various calculations while preserving the data confidentiality. Here we apply the homomorphic encryption scheme proposed by Brakerski and Vaikuntanathan (CRYPTO 2011) to secure statistical analysis between two variables. For reduction of ciphertext size and practical performance, we propose a method to pack multiple integers into a few ciphertexts so that it enables efficient computation over the packed ciphertexts. Our packing method is based on Yasuda et al.’s one (DPM 2013). While their method gives efficient secure computation only for small integers, our modification is effective for larger integers. Our implementation shows that our method is faster than the state-of-the-art work. Specifically, for one million integers of 16 bits (resp. 128 bits), it takes about 20 minutes (resp. 3.6 hours) for secure covariance and correlation on an Intel Core i7-3770 3.40 GHz CPU.