In a statement announcing his resignation, Mehmet Ali Yalcindag denied that the emails leaked on social media this week by the leftist RedHack group had come from him, and vowed to take legal action. He described the act as an "ugly scam".
The resignation of the head of a group whose titles include leading newspaper Hurriyet, broadcaster CNN Turk and mainstream television channel Kanal D, comes amid concern about pressure on the media in Turkey, particularly since emergency rule imposed after a failed July coup, gave the authorities sweeping powers.
More than 100 journalists have been detained since July 15, when soldiers commandeered tanks and fighter jets in a bid to seize power, on suspicion of links to the network blamed for the coup. Wider purges have meanwhile seen some 100,000 police, soldiers, judges and civil servants sacked or suspended.
Yalcindag said he was resigning to prevent damage to the reputation of parent company Dogan Holding, one of Turkey's best-known family conglomerates, with interests ranging from media and real estate to energy and retail.
"I have decided to leave this post, which I have occupied with dedication and care since the beginning of this year, to prevent the allegations directed at me from harming the reputation of the Dogan group," he said.
The alleged emails released by RedHack included correspondence supposedly between Yalcindag and Erdogan's son-in-law, Energy Minister Berat Albayrak, in which the Dogan executive appears to show willingness to adjust the editorial line of Dogan brands to appease the government.
Officials in Albayrak's office declined to comment.
Dogan Holding shares dropped as much as 3.6 percent on Friday, after falling around 3.5 percent on Thursday.
"In the technical inspections on my personal computer, it was uncovered that these e-mails were not sent by me, and were not sent through my computer. This is an ugly scam," Yalcindag said in his statement.
"Charlatans"
In the latest media closures following the coup, Turkey has ordered 20 television and radio stations shut down, including one that airs children's programmes, on charges they spread "terrorist propaganda".
Prominent journalist Ahmet Altan, also a popular novelist, was detained for trial last week, accused of participating in the coup by sending out subliminal messages to the troops who tried to seize power.
Officials reject the notion that the actions are a bid to stifle dissent, saying the extent of the crackdown is justified by the gravity of the threat to the state. Those found not to have links to the coup will be released, they have said.
Dogan Holding has long had a tense relationship with Erdogan and the ruling AK Party.
In May, Dogan was suspended from state tenders after Erdogan accused its head, Aydin Dogan, of being a "coup lover" and described its media columnists as "charlatans".
In 2009, Dogan Media was fined $2.5 billion for unpaid taxes, in what government opponents saw as an attempt to crush media criticism of Erdogan, following its coverage of corruption allegations against members of his inner circle.
Following the tax bill, founder Dogan was forced to sell the group's Milliyet and Vatan newspapers, the Star TV channel and other holdings.
In a statement shortly after Yalcindag's resignation, Aydin Dogan, honorary president of Dogan Holding, said the unity of the Dogan family would not be affected.
"(Dogan Media) has stood tall against all kinds of impositions, including times when democracy was suspended, and has paid grave prices," he said. "We are determined to continue our broadcast policy in accordance with our principles."
