A document management system comprises a document management apparatus that manages a document ID by associating the document ID with a storage time of the document, and checks the storage time in response to an inquiry about a permission of destroying the document and gives a permission of destroying the document when the storage time has expired, and a document destruction apparatus including a mode selection unit that selects one of a first destruction mode and a second destruction mode and an execution unit that destroys the document according to a destruction mode selected by the mode selection unit. The execution unit destroys the document without reading the document ID in the first destruction mode, and reads the document ID to inquire the permission of destroying the and destroys the document when the document management apparatus gives the permission of destroying the document in the second destruction mode.