Turkish riot police have fired plastic bullets and tear gas to disperse hundreds of protesters who gathered outside the offices of Zaman newspaper in Istanbul, a day after it was seized by authorities.

The officers set up barricades on Saturday outside the headquarters of Turkey's largest-circulation daily, which has been reopened under government control.

A court on Friday appointed an administrator to run the flagship Zaman, English-language Today's Zaman and Cihan agency, linked to Fethullah Gulen, a US-based influential political opponent of President Recep Tayyip Erdogan.

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.

The court ruling came at the request of a prosecutor investigating Gulen on terrorism charges, state media said.

Employees returned to the newsroom on Saturday to work under the new administrator, but Abdulhamit Bilici, Zaman's editor-in-chief, and Bulent Kenes, a columnist, were fired and escorted from the premises, said Sevgi Akarcesme, top editor at Today's Zaman.

"It is a dark day for Turkish democracy and a flagrant violation of the constitution," Akarcesme told Reuters news agency.

He said most Turkish media were not fully reporting the takeover out of fear they could face similar reprisals.

'A dark period'

Staff took to social media to post photos of armed special forces inside the building and also guarding the barricaded perimeter after police raided the offices.

"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," Bilici had earlier said.

"This is a dark period for our country, our democracy."

Today's Zaman's Saturday edition, published before the takeover, printed its entire front page in black with the headline: "Shameful day for free press in Turkey."

"We are here to defend democracy and freedoms," one protester told Al Jazeera.

Prosecutors accused Zaman and its affiliates of praising and helping what they called a "terrorist organisation".

"There is some obvious evidence that they [Gulen and Zaman] are linked to many international organisations," Yasin Aktay, a member of Turkey's ruling AK party, told Al Jazeera.

"And Zaman newspapers and others are part of this coordination with this apparatus."

Aktay rejected allegations about media intolerance by the Turkish government.

"There is no intolerance in Turkey about media criticism. [There's] probably more than 60 or 70 percent of the media in Turkey against the government and the government is tolerating them," he said.

For his part, Robert Pearson, a former US ambassador to Turkey, told Al Jazeera the move to take over the newspaper was not unexpected.

READ MORE: Journalists accused of 'terrorism' released in Turkey

"Mr Erdogan refers to almost anyone who opposes his rule as a terrorist - college professors, journalists - anyone who basically disagrees with him," Pearson said.

Erdogan has repeatedly insisted Turkey has the most free media in the world, but the country consistently ranks poorly on press freedom indices.

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.