At least 12 Cumhuriyet employees affected by decision described by government as arising from probe launched in August.
Turkish police have detained at least a dozen people working for the opposition Cumhuriyet newspaper, according to news-media reports.
Cumhuriyet said that along with Murat Sabuncu, the editor-in-chief, 13 other other employees of the paper, including its managing staff, writers and executives, were detained on Monday.
State-run Anadolu Agency said 12 people from Cumhuriyet were detained, adding that their homes were searched.
The detentions come as authorities crack down on anyone suspected of links to Fethullah Gulen, the US-based religious leader accused by the Turkish government of orchestrating a failed coup in July.
A statement by the Istanbul prosecutor’s office said the media employees had taken into custody for having alleged links to Gulen and the outlawed armed Kurdistan Workers’ Party (PKK).
Numan Kurtulmus, a government spokesperson, said on Monday the detentions were the result of an investigation initiated in August.
He also said that it was not possible for politicians to comment on the process.
"There is an ongoing legal process. We will all follow this legal process," he said.
Scores of opposition media organisations have been shut down since the government acquired emergency powers following the failed coup, including pro-Kurdish ones such as IMC TV, the Dicle news and the Ozgur Gundem newspaper.
More than 100,000 people had already been sacked or suspended and 37,000 arrested since the coup attempt.
Over the weekend, Turkey dismissed a further 10,000 civil servants and closed 15 more media outlets over suspected links with armed groups and Gulen.
Cumhuriyet said its staff had their laptops seized from their homes after police search.
Footage showed one writer, Aydin Engin, 75, being ushered by plainclothes police into a hospital for medical checks.
Asked by reporters why he was detained, Engin said: "I work for Cumhuriyet, isn’t that enough?"
Another veteran journalist, Kadri Gursel, who began writing for Cumhuriyet in May, said on Twitter that his house was being searched and that there was an arrest warrant for him.
Readers of the daily gathered in masses at the Cumhuriyet headquarters in Istanbul to protest the operation.
Cumhuriyet, known for its critical stance towards the government, got wide international attention in 2015 when it reported on a fleet of Syria-bound trucks allegedly sent by the country’s intelligence agency, carrying weapons to Syrian anti-government fighters.
Can Dundar, Cumhuriyet’s previous editor-in-chief, was sentenced to six years for publishing state secrets for that report.
Dundar, who lives in Germany now, has ruled out returning to Turkey until the emergency measures are abolished.
He is among the people prosecutors issued arrest warrants for on Monday.
While Turkey insists it is acting within the rule of law, organisations defending free speech have accused the government of violating human rights.
"Restrictions imposed under the state of emergency go beyond those permissible under international human rights law, including unjustifiable limitations on media freedom," Reporters Without Borders and other rights groups said earlier this month.