It is understood that he will not be replaced as the company looks to rejig its management team.
Milner was part of the team that made Newsprinters, the company's print business, an independent subsidiary and played a key role in the building of the three print plants at Eurocentral, Knowsley and its flagship Broxbourne plant.
With former executive chairman Les Hinton and operations director Ian McDonald, along with a number of other high profile managers, having already moved on Milner represented the last of the key players in News International's move from Wapping in the early part of the millennium.
One industry source said: "They've moved the old guys on, it’s the youngsters' turn now."
Rupert Murdoch, chairman and chief executive officer of News Corporation, said: "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.
"Clive is a professional newspaperman of the highest calibre who has served both his company and the whole industry in the UK with distinction. We all wish him well in the future."
Milner is also currently chairman of News Media Coalition campaigning body the Newspaper Publishers Association, as well as a board member at Pressbof, the funding body for the Press Complaints Commission. It is understood that he will continue in these roles.
