Unfortunately, once a document has been published in the public setting on issuu, it cannot be changed to an unpublished one, as the publication's details are already public on the web, and has been indexed by various search engines.
To resolve this,
1. Download the publication that has been made public and delete it from your issuu account.
2. Change the file name of the document you downloaded (the file name becomes part of the document link), then upload it as an unlisted publication. This will give the publication a different document link and ID. The stats and impressions from the old documents (the ones that were public) will not carry over to these new documents.
Also, once deleted, people who have already seen the public versions will no longer be able to access that publication.