Mehmet Ali Yalcindag had since last year been the head of the Dogan Media Group which groups together key interests including the Hurriyet newspaper, CNN-Turk news channel and Kanal-D channel.
The newspaper and channels are generally seen as independent of the government while taking care not to follow an overtly oppositional line.
However, Yalcindag's position came under scrutiny when emails purportedly written by him were released on social media by a group calling itself Redhack.
In a statement published on the website of Hurriyet, Yalcindag denied the authenticity of the emails and said he was victim of an "ugly fraud".
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"A technical analysis of my personal computer has revealed that the emails were not written by me and were not sent using my computer."
He added: "I will use every legal right available to me against these publications," saying that detailed analysis would be carried out to explain what happened.
In the purported emails, Yalcindag is alleged to complain of Hurriyet's editor-in-chief Sedat Ergin and details plans to force him out.
Ahmet Hakan, a Hurriyet columnist, and Hande Firat, CNN-Turk's Ankara bureau chief, are cited as "reliable" names to replace him.
Aydin Dogan, the founder of the family-controlled Dogan Group, said he respected the decision of Yalcindag, who is also his son-in-law.
The tycoon said he considered it an "offense" to access personal data through illegal means and present it through manipulation.
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