The Sage separated the Juubi into 9 parts, but removed the shell of the Juubi (Gedo Mazo) and buried it within the Moon using Chibaku Tensei. He wanted this away from other shinobi the most out of everything else he did (because the Gedo Mazo is the one that takes in the chakra of the biju and becomes the Juubi again. Without this, you have no Juubi).
Little did he know that one such shinobi would gain the powers of his other half and be able to summon it again (Madara)!