A method of performing a homomorphic permutation by a server includes: generating, via a ciphertext generation portion, a first ciphertext by adding noise to the basic ciphertext; transmitting, via a transmission portion, the first ciphertext to a client; performing, via an operation portion, a predetermined operation on the noise; receiving, via a reception portion, a second ciphertext from the client; and extracting, via an extraction portion, the basic ciphertext on which the predetermined operation is performed, by removing, from the second ciphertext, the noise on which the predetermined operation is performed, wherein the second ciphertext is a ciphertext that is re-encrypted by the client after decrypting the first ciphertext and performing the predetermined operation on the decrypted first ciphertext.