Milner, who oversaw operations across News International titles including The Times, News of the World and The Sun, will leave at the end of the year. It is not thought that he will be replaced directly.
News International has made several changes to its senior management team this year including promoting Katie Vanneck-Smith on to its executive team and handing her the title chief marketing officer.
It also recruited former chief operating officer of Discovery Television Networks, David Rey to the new role of chief business officer and executive team member.
Milner is said to have been responsible for developing News International’s print plants at Broxbourne, Knowsley and Eurocentral and overseeing a new distribution network.
Rupert Murdoch, chairman and chief executive officer of parent company News Corporation, says: “Clive has been my colleague at News International for 30 years and in that time I have had great regard for the skill with which he helped create the successful company we see today.”