Police using tear gas and water cannon raided the headquarters of Turkey's largest-circulation newspaper, hours after a court placed it under the management of trustees.
Police set up barricades on Saturday to keep out Zaman readers arriving at the building in a show of support.
The English-language Today's Zaman Saturday edition, published before the forced take-over, printed its entire front page in black with the headline: "Shameful day for free press in Turkey."
Prosecutors accused Zaman and its affiliates of praising and helping what they called a "terrorist organisation".
"It has been a habit for the last three, four years, that anyone who is speaking against government policies is facing either court cases or prison, or such control by the government," said Abdulhamit Bilici, editor-in-chief of Zaman.
"This is a dark period for our country, our democracy."
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The daily is associated with a movement led by US-based Muslim cleric Fethullah Gulen, an influential political opponent of President Recep Tayyip Erdogan.
State-run Anadolu Agency reported on Friday that administrators had been appointed by a court to run Zaman at the request of an Istanbul prosecutor. Officials were not immediately available to confirm the reports.
Erdogan accuses Gulen of conspiring to overthrow the government by building a network of supporters in the judiciary, police and media. Gulen has denied the allegations.
Erdogan and Gulen were allies until police and prosecutors seen as sympathetic to Gulen opened a corruption probe into Erdogan's inner circle in 2013.
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Robert Pearson, a former US ambassador to Turkey, told Al Jazeera the move to take over the newspaper was not unexpected.
"Mr Erdogan refers to almost anyone who opposes his rule as a terrorist - college professors, journalists - anyone who basically disagrees with him," Pearson said.
John Kirby, a US State Department spokesman, called the Turkish government's action "troubling".
The New York-based Committee to Protect Journalists (CPJ) also said it was "alarmed" by the government's decision.
"Today's move by the court paves the way to effectively strangle the remnants of critical journalism in Turkey," CPJ Executive Director Joel Simon said in a statement.
Erdogan has repeatedly insisted Turkey has the most free media in the world, but the country consistently ranks poorly on press freedom indices.
Zaman is Turkey's biggest selling newspaper, with a circulation of 650,000 as of the end of February, according to media-sector monitor MedyaTava website.
Hundreds of supporters gathered in the rain outside Zaman's Istanbul office on Friday night to condemn the move and were dispersed by riot police who fired tear gas and water cannon.
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The crackdown on Zaman comes at an already worrying time for press freedom in Turkey.
Two prominent journalists from the pro-opposition Cumhuriyet newspaper are facing potential life sentences on charges of endangering state security for publishing material that purports to show intelligence officials trucking arms to Syria.
| Turkey's 'free' press - The Listening Post
Source: Al Jazeera and agencies