Police stormed the editorial headquarters of Zaman, Turkey's largest opposition newspaper, and fired tear gas to disperse protesters who had gatherd outside the building late Friday in Istanbul, Turkish media reported online.
Earlier, staff at the media house prepared their last edition Friday before a government-appointed trusteeship took court-ordered control of the paper and replaced the management. A headline in the last edition screamed: "Get out, thieves."
The trusteeship will assume control of the paper following a court order requested by a prosecutor. Zaman has editions in several languages, including Turkish and English.
A report by the state-run Anadolu news agency did not cite a reason for the court order.
Employees of the newspaper in Istanbul confirmed the information to dpa by telephone earlier Friday, noting that they were not aware of the specific charges against the media house.
"We are working on the last issue of our newspaper," Sevgi Akarcesme, the editor-in-chief of Today's Zaman, the English-language version of the paper, told dpa.
"The government has seized our newspaper," she said,
"This is the end of media freedoms in Turkey, and this is against our constitution. This is a sad and shameful day."
International rights groups and journalism watchdogs denounced the action.
The Turkish government's move reflected an "ongoing onslaught on dissenting media," Amnesty International said.
"By lashing out and seeking to rein in critical voices, President Erdogan's government is steamrolling over human rights," said Andrew Gardner, Amnesty's Turkey expert.
As the paper was facing closure, EU President Donald Tusk met with Turkish President Recep Tayyip Erdogan in Istanbul.
Zaman, which according to its own data averaged 850,000 daily print copies last year, is accused of being part of the network of Fethullah Gulen, an Islamic preacher based in the US.
Gulen was a one-time ally of Erdogan, but the two fell out recently and the government has pushed the line that the preacher's movement, known as Hizmet (Service), is a terrorist group. He is accused of running a "parallel" state within the civil service.
Alleged Gulenists are accused of a range of crimes, including illegal wiretapping. Hundreds of alleged Hizmet members have been arrested on a range of charges.
"It is absolutely illegitimate and intolerable that Erdogan has used the judicial system to take control of a great newspaper in order to eliminate the Gulen community's political base," said Reporters Without Borders secretary general Christophe Deloire.
"This ideological and unlawful operation shows how Erdogan is now moving from authoritarianism to all-out despotism."
Opponents of the Gulenists from other elements of the opposition have accused the group of helping authorities crack down on critics during the lengthy era when the movement was close to Erdogan.
"The appointment of trustees over Zaman newspaper is an important step in the fight against the parallel structure. They pay the price for the infidelity towards the state and the people," said Emrullah Isler, a member of parliament from Erdogan's Justice and Development Party (AKP).
The government has taken over other critical media outlets allegedly affiliated with Gulen, amid charges by rights groups that press freedoms are facing a sustained attack in Turkey.
Zaman editor-in-chief Ekram Dumanli was arrested in 2014 and accused of terrorism-related charges, before being released because of lack of evidence.
The leftist Cumhuriyet newspaper saw its editor-in-chief and Ankara correspondent arrested in November after they reported on Turkey's spy agency sending weapons to militias in Syria. Can Dundar and Erdem Gul from Cumhuriyet were held for three months and released last week under a Constitutional Court order.
Erdogan, who vowed that the journalists would pay a "heavy price" for their reporting, lashed out at the court following the release.
"I am not in a position to approve the ruling. I neither obey nor respect the ruling," Erdogan said, while pro-government media outlets criticized the court decision.
Zuhtu Arslan, head of the court, has been on the defensive this week, condemning a campaign of "lies" against the Constitutional Court.
Erdogan has repeatedly insisted Turkey has the most free media in the world, but the country consistently ranks poorly on press freedom indices.
Turkey is seeing a wave of arrests targeting people who allegedly "insult" the president. Nearly 1,850 cases have been opened against suspects who were critical of the president, the justice minister said this week, noting that freedom of expression did not include the right to insult.