A simple solution that lets commentators easily establish private comment threads is the wpDiscuz Private Comments extension. The topic owners, moderators, and website administrators will all have access to these threads. In order to make a comment private, the add-on adds a little button right next to the submit button.
It also adds a “Private” button to parent comments once the comment has been posted. In the dashboard, the buttons to mark comments as private may be shown or hidden depending on the user role. Additionally, it enables setting up specific user roles to control private comments. In the event that you have many custom comment forms for unique post types, this capability may be activated or disabled for a specific comment form.