The Turkish daily Zaman, the country’s biggest newspaper, has published its first printed edition under new management, two days after the government seized the paper and removed its editor-in-chief.

Formerly an opposition newspaper critical of the Turkish president, Recep Tayyip Erdoğan, and his Justice and Development party (AKP), Sunday’s edition firmly toed the government line.

“In less than 48 hours, the new admin turned seized Zaman into a propaganda piece of the regime in Turkey,” Sevgi Akarcesme, the editor-in chief of Today’s Zaman, an English-language sister publication, tweeted.

On Friday a Turkish court ruled that the newspaper should be run by appointed trustees. A reason for the decision was not given.

“We are going through the darkest and gloomiest days in terms of freedom of the press, which is a major benchmark for democracy and the rule of law,” a statement published by Today’s Zaman read. “Intellectuals, businesspeople, celebrities, civil society organisations, media organisations and journalists are being silenced via threats and blackmail. We have entered the last phase in terms of pressure on those who persistently remain independent in their publications.”

On Sunday, former Zaman staff set up a newspaper, Yarina Bakis, meaning “look towards tomorrow”, with Zaman’s former Twitter feed automatically redirecting readers to the new account.

The paper’s website featured a message promising readers “high quality and unbiased” content “as soon as possible” on Sunday.

Only hours after the court ruling on Friday, police used teargas and rubber bullets against protesters who had gathered in front of the newspaper and later forced their way into the building to raid the offices. Officers forcefully removed protesters on Saturday, and newspaper staff arriving for work had to enter the building under tight police control.

Police at the headquarters of Zaman in Istanbul on Sunday. Photograph: Emrah Gurel/AP

On Monday leaders of EU member states will meet with Turkish counterparts in Brussels for a crucial summit to discuss the implementation of a contentious migration deal. Under the proposals, the EU will pledge financial aid and political concessions in return for Turkey’s promise to help decrease the flow of refugees to Europe.

The Turkish government has insisted that it was not involved in the court ruling, and the prime minister, Ahmet Davutoğlu, has called the paper’s confiscation a “legal procedure”, adding that it was “not political”.

The newspaper is closely associated with the movement of Fethullah Gülen, a US-based Islamic cleric and a former ally of Erdoğan who has since become a fierce critic, especially over diverging views on the government’s handling of the 2013 Gezi protests and the AKP’s Syria policy.

The two men fell out over a corruption scandal that broke in December 2013 and implicated senior government officials, Erdoğan’s closest associates and his family.

Erdoğan has repeatedly accused Gülen of having established a “parallel structure” within the state by placing his followers in institutions such as the judiciary and the police, and of exerting strong influence through his media empire. Turkish authorities have labelled the movement, known as “Hizmet” among its millions of followers worldwide, a “terrorist organisation”, known in Turkey under the acronym FETÖ. Gülen has denied any plans to overthrow Erdoğan or the Turkish government.

In October last year, government trustees were appointed to manage the Koza İpek Media Group, a business with close ties to the Gülen movement. Last month, the group’s media operations, including TV channels and newspapers, were closed down. Two other opposition TV channels were taken off air two weeks ago.

Human Rights Watch and Amnesty International have both harshly condemned the takeover of the daily Zaman.

“The Istanbul court’s decision to appoint trustees to run Zaman newspaper and other media is nothing but a veiled move by the president to eradicate opposition media and scrutiny of government policies,” said Emma Sinclair-Webb, senior Turkey researcher for Human Rights Watch, in a statement at the weekend. “This deplorable ruling, which follows the blocking of two critical TV stations, is the latest blow to free speech in Turkey.”

Earlier this week Erdoğan said he would neither “recognise nor respect” the ruling by the constitutional court to release Can Dündar, the editor-in-chief of the opposition newspaper Cumhuriyet and the paper’s Ankara bureau chief Erdem Gül from jail. Both have been in prison pending trial since last November on charges of espionage over articles claiming that the AKP government had shipped arms to Islamist groups in Syria. Both journalists still face terrorism charges and are banned from leaving the country.

While Erdoğan maintains that the press in Turkey is among the most free in the world, human rights organisations and media monitoring groups have warned that freedom of expression is under ever growing pressure, and has lately been in freefall. Turkey ranks 149th among 180 countries in the World Press Freedom Index published by Reporters Without Borders.