A secure joining system is a secure joining system including a plurality of secure computing apparatuses. The plurality of secure computing apparatuses include a vector joining unit 11n, a first vector generation unit 12n, a first permutation calculation unit 13n, a first permutation application unit 14n, a second vector generation unit 15n, a third vector generation unit 16n, a second permutation calculation unit 17n, a second permutation application unit 18n, a fourth vector generation unit 19n, a fifth vector generation unit 110n, a first inverse permutation application unit 111n, a first vector separation unit 112n, a second inverse permutation application unit 113n and a second vector separation unit 114n, a third permutation application unit 115n, a fourth permutation application unit 116n, and a first joined table generation unit 117n.