By Ayla Jean Yackley

ISTANBUL (Reuters) - Turkish police fired tear gas and rubber bullets on Saturday to disperse protesters outside the country's biggest newspaper after authorities seized control of it in a crackdown on a religious group whose leader the government accuses of treason.

A court on Friday appointed an administrator to run the flagship Zaman, English-language Today's Zaman and Cihan agency, linked to U.S.-based cleric Fethullah Gulen, who President Tayyip Erdogan says was plotting a coup.

Rights groups and European officials condemned the takeover, seeing it as proof that Turkey's government silences dissident views. Other media outlets affiliated with Gulen's movement were taken over in October, and companies including a bank have been seized, wiping out billions of dollars in valuations.

"Turkey has the right to question those who take part in a clear coup attempt, whether economic or journalistic, against an elected government," Prime Minister Ahmet Davutoglu said while on a trip to Tehran.

"There is a legal process examining charges of political operations, including funneling illegal monies. We have never intervened in the legal process," he said.

Erdogan has repeatedly pledged to crush Gulen's conservative religious movement, which he said has infiltrated the police, judiciary and bureaucracy since his party won power in 2002.

"Extremely worried about latest developments on Zaman newspaper which jeopardizes progress made by Turkey in other areas," European Enlargement Commissioner Johannes Hahn said on Twitter.

European Parliament President Martin Schulz tweeted the takeover was "yet another blow to press freedom" and said he and Davutoglu would discuss it on Monday.

Critics have accused the European Union of turning a blind eye to Turkey's rights record because it needs Ankara's help curbing huge flows of refugees and migrants.

Turkey, which borders Syria, Iraq and Iran, will join EU leaders in Brussels at a crisis summit on Monday. Davutoglu said the "positive agenda will now be occupied and stained" with the issue of press freedom.

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"Any country, and in particular those negotiating EU accession, needs to guarantee fundamental rights, including freedom of expression, and due judicial process, in line with the European Convention on Human Rights," the European Commission said in a statement.

SACKINGS

Police first raided Zaman around midnight, firing tear gas and water cannon and forcing open a gate to enter the offices. Employees returned to work on Saturday under the new administrator but editor-in-chief Abdulhamit Bilici and columnist Bulent Kenes were fired, 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, adding most media were not fully reporting the takeover for fear of similar reprisals.

Kemal Kilicdaroglu, head of the main opposition Republican People's Party, said the court was acting as a political tool.

Zaman's editors were largely supportive of Erdogan during much of his party's rule since 2002, but they fell out over foreign policy and a move to close schools run by the Gulen movement, a source of much of its influence and income.

Then police thought to follow Gulen's teachings leaked news of a corruption investigation into Erdogan's inner circle in December 2013, which Erdogan described as a coup attempt.

The raid on Zaman and its sister publications was "nothing but a veiled move by the president to eradicate opposition media and scrutiny of government policies," said Emma Sinclair-Webb, Human Rights Watch's senior Turkey researcher.

In Berlin, ruling party lawmaker Norbert Roettgen said: "Not only the violent action against a critical newspaper, but also the fact that the government takes over the whole paper is a severe blow by the Turkish leadership against the freedom of press."

(Additional reporting by Osman Orsal and Melih Aslan in Istanbul, Michael Nienaber in Berlin and Foo Yun Chee in Brussels; Writing by Ayla Jean Yackley; Editing by Adrian Croft and Hugh Lawson)