CAIRO—Journalists and rights advocates in Egypt are renewing concerns about the contraction of freedom of expression after police arrested four Al Jazeera English journalists during a raid on the Cairo hotel suite they used as an office on Sunday, removing the last physical outpost of the Qatar-based network in the country.

The journalists, Bureau Chief Mohamed Fahmy, Peabody-award winning Australian journalist Peter Greste, freelance producer Baher Mohamed, and cameraman Mohamed Fawzy, were arrested after authorities entered their suite in the Marriott with an arrest warrant, according to Ragia Omran, an attorney representing the journalists. Fawzy was later released.

Omran said that during questioning in Cairo’s Tora Prison on Wednesday, interrogators asked Greste about his reporting in Egypt, including a report he was working on about Muslim Brotherhood-affiliated charities in a Cairo slum. (Last week the government officially declared the Brotherhood a “terrorist” organization, a designation that could shut down the movement’s massive network of social services.)

The arrests were the latest in a series of incidents highlighting the loss of freedom of expression in Egypt. Last month, a court sentenced three prominent activists to three years in prison for violating a new law criminalizing all protests that take place without explicit government permission. The new military led-government has censored three Islamist news channels, and Egyptian journalists once again speak of implicit “red lines” circumscribing what they can and cannot print. “We’re facing a problem not just with the media. Activists, citizens, anyone who is willing to speak out or do anything that is against the current regime and the current political will is going to be cracked down upon. It’s a very clear message,” Omran said.

On Tuesday, Egypt’s general prosecutor ordered the three journalists held for another 15 days while investigations proceed. According to Omran, the three are facing a range of charges, including “spreading false news” and “broadcasting externally with intention of threatening national security.” Fahmy is also accused of belonging to the Muslim Brotherhood, which is now branded a terrorist organization. The charges against Baher Mohamed have not yet been confirmed, Omran said.

In January 2011, much of the English-speaking world looked to AJE, not to be confused with the brand new US-based Al Jazeera America, during its extensive coverage of the 18-day popular uprising that toppled dictator Hosni Mubarak. Today, the network’s fortunes have changed. During the yearlong presidency of Muslim Brotherhood member Mohamed Morsi, the network, in particular its Egypt-based Al Jazeera Mubasher Misr, became perceived as sympathetic to the Islamists. After the military removed Morsi from power in July, authorities raided the offices of Al Jazeera Arabic, and Al Jazeera Mubasher Misr was banned by court order. After weeks of street harassment and last summer’s raid, the English channel moved its operation to the Marriott out of concerns for its staff’s security.

AJE staff completely reject the notion of bias in their reporting. “Peter Greste, Mohamed Fahmy, and Baher Mohamed are just journalists doing the same work as colleagues from other foreign broadcasters based in Cairo,” said Bernard Smith, an AJE correspondent who has worked regularly in Egypt. AJE has “bent over backwards to make sure we present a balanced view of the developments in Egypt.”

Smith suggested that the timing of the arrest was related to the fact that Egypt is approaching the third anniversary of the January uprising. “Both AJE and AJA are widely watched in Egypt, so our coverage was credited by some as having contributed towards the momentum that ultimately forced Mubarak from the presidency,” he said in an email. “Perhaps the military-backed government doesn’t want to something like that happening again.”

Meanwhile, Fahmy’s family strenuously denied the charges against him. “The whole family is anti-Muslim Brotherhood,” said his brother Sharif, reached by phone in Kuwait. “We come from a very liberal family. Both our grandfathers were with the Egyptian police force.” Fahmy and his two brothers were raised in Canada. After attending a university in Calgary, he went on to work for The New York Times, the Red Cross, and CNN. “We are the total opposite of the Muslim Brotherhood ideology,” said Sharif Fahmy.

Fahmy fell and injured his shoulder prior to the raid, and it broke due to the “dismal condition” of a vehicle he was transported in after the arrest, Omran said, adding that he is sleeping on the floor of a concrete cell in Tora prison. The three detainees are being held in separate cells in a wing where several high-profile members of the Muslim Brotherhood are also held, Omran added. “They’re in the hardcore prison,” she said.

The arrests also come after the Committee to Protect Journalists identified Egypt as one of the top 10 jailers of journalists, and the third deadliest country for journalists, after Syria and Iraq, in 2013. According to CPJ, at least five other journalists are in custody in Egypt, including two affiliated with Al Jazeera: cameraman Mohamed Bader and correspondent Abdullah al-Shami.

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Jared Malsin is a freelance journalist based in Cairo