Sabuncu's arrest also came as the government fought an insurgency from the outlawed Kurdistan Workers' Party
Turkish police detained the editor-in-chief of the opposition newspaper Cumhuriyet, state media reported Monday, while CNN Turk said 13 arrest warrants were issued for journalists and executives from the daily.
Murat Sabuncu was detained while authorities searched for executive board chairman Akin Atalay and writer Guray Oz, the official news agency Anadolu said.
The daily said Oz had already been detained.
Police were searching the homes of Atalay and Oz, Anadolu said.
The latest detentions came as authorities pressed a massive crackdown over a failed July bid by a rogue faction of the military to oust President Recep Tayyip Erdogan.
Tens of thousands of civil servants have since been suspended, fired or detained, with the government pointing the finger of blame for the coup bid at exiled Muslim preacher Fethullah Gulen.
The government has also shut more than 100 media outlets and detained dozens of journalists as it presses a purge that has come under fire by Western leaders and human rights organisations.
Sabuncu's arrest also came as the government fought an insurgency from the outlawed Kurdistan Workers' Party (PKK).
The government's operation against the Cumhuriyet daily was launched over its alleged "activities on behalf of" the Gulen movement and the PKK.
The PKK -- proscribed as a terrorist organisation by Ankara, the EU and US -- has waged an insurgency inside Turkey since 1984.
Cumhuriyet's former editor-in-chief is Can Dundar, who was sentenced in May by a Turkish court to five years and 10 months in prison for allegedly revealing state secrets.
Dundar is now believed to be in Germany after he was freed earlier this year pending an appeal.