Fox promoted James Murdoch to chief executive in June, giving him day-to-day control of the company, and made Lachlan Murdoch executive co-chairman.
Ailes has been one of a few top Fox executives to report directly to Rupert Murdoch, and said this month that he expected to keep doing so, even after the 84-year old media baron moved from CEO to chairman.
"My job is to report to Rupert, and I expect that to continue," Ailes was quoted as saying by Variety magazine on June 11, the same day reports of James and Lachlan's impending promotions emerged.
Ailes has been with the company since 1996 and oversaw the creation and launch of Fox News Channel, which currently reaches more than 90 million homes.
He was made chairman of Fox Television Stations Group in 2005, a few months after Lachlan — seen as the heir apparent — resigned as deputy chief operating officer of News Corp.
A difference of opinion with Ailes was one of the factors behind Lachlan's exit, according to media reports at the time.
"Roger and I have always had, and will continue to have, a special relationship," Rupert said in a statement on Thursday.
Fox could not be immediately reached for further comment.
(Reporting by Amrutha Penumudi and Supantha Mukherjee in Bengaluru; Editing by Simon Jennings)
