Supporters of the Muslim Brotherhood gather in Cairo on April 24, 2015. (Belal Darder/AP)

A year ago, Mohamed Zarea ran a successful nonprofit group in a sprawling office in central Cairo, with 50 employees providing legal and medical aid to Egyptian prisoners.

Now, Zarea and just three remaining staff members operate out of a small apartment with a leaky roof in a rundown suburb. They have halted most of their assistance to detainees. Egyptian authorities recently blocked Zarea’s access to more than $50,000 from the European Union, he said, crippling his 18-year-old organization, the Human Rights Association for the Assistance of Prisoners.

Barely noticed in a region engulfed in multiple wars, Egypt’s crackdown on civil society groups is escalating well beyond the repressive measures taken by ousted president Hosni Mubarak, human rights groups say.

In recent months, authorities have harassed rights advocates, intercepted grants for nonprofits such as Zarea’s and enforced legislation that would subject such groups to strict government surveillance.

Officials say the organizations need to be monitored to ensure that they are not working against the nation’s interests. But critics say the clampdown has devastated groups that are vital to creating democracy in an increasingly authoritarian state.

Supporters of Egypt's former president Hosni Mubarak gather outside the Maadi military hospital for his birthday on May 4, 2015. (Mohamed El-Shahed/AFP/Getty Images)

The government campaign intensified with an ultimatum last fall for civil society groups to register with authorities. Many such organizations have registered in the past as law firms or private companies to avoid the coercive restrictions they say come with filing for official status with the government.

“There are very clear attempts by the government to eliminate human rights work in Egypt at a time of some of the worst human rights violations,” said Mohamed Zaree, program director at the Cairo Institute for Human Rights Studies.

The institute, which is registered as a research company, recently moved its program that monitors regional human rights abuses to Tunisia. But activists say even groups that are undergoing the arduous registration process with the government face persecution.

The government recently slapped travel bans on employees of the Egyptian Democratic Academy, a nonprofit youth group, preventing its members from going abroad, even though it had filed an application for registration with authorities last fall. Such actions have forced other groups to lay off employees, reject grants from foreign donors or move activities abroad.

Under a decree issued last year, anyone who receives foreign funding with the aim of harming Egypt’s “national interests” can face a life sentence in prison.

“It actually doesn’t matter if you register or not. It’s about the type of activities your organization is involved in — if the government approves of them or not,” Zaree said in an interview. “We are working in an environment that is worse than it was under Mubarak. We really are fighting for our survival.”

Under Mubarak, who was toppled in a pro-democracy revolt four years ago, authorities restricted civil society groups but gave activists a measure of leeway to carry out their work.

Mubarak, activists say, was far more concerned with criticism from the United States and other countries than is Egypt’s current president, Abdel Fattah al-Sissi.

After the Arab Spring rebellion in 2011, donors — including the U.S. government — poured money into pro-democracy and human rights organizations working to train civil society activists and election monitors.

Following the revolution, “there was a political sphere. There were human rights violations, but there were open spaces,” Zaree said. “There were political parties, social movements and a parliament. Even if there were government threats, we could actually survive and work quite well in that environment.”

But some government officials were suspicious that Egyptian civil society groups fostered the country’s uprising. When Sissi came to power in a coup in 2013, he consolidated control, jailing tens of thousands of people and painting detractors as enemies of the state.

As part of the push to crush dissent, authorities set their sights on nonprofits, most of which rely on foreign grants to stay afloat. Egypt’s domestic spy service, the Homeland Security agency, was granted an expanded role in approving or rejecting such donations and in investigating the activities of Egyptian recipients of such support, rights advocates and officials say.

Authorities have said the regulations have been put in place to catch funds that are funneled to charities linked to the Muslim Brotherhood, an opposition movement that the government declared a terrorist organization in 2013. Former president Mohamed Morsi, who was ousted in the coup, was a member of the movement.

But in a dossier recently prepared by Egypt’s Homeland Security agency, Islamists did not appear to be the only targets. It said that a number of civil society groups, including human rights organizations, were working on behalf of unidentified foreign governments to defame Egypt. The dossier’s contents were disclosed this month by the daily Egyptian newspaper al-Shorouk.

The Ministry of Social Solidarity, which handles the registration of nonprofit and civil society groups, did not respond to multiple requests for comment.

But a former senior official at the ministry, who now works elsewhere in the cabinet, said that the ministry relies heavily on Homeland Security to monitor nongovernmental organizations.

In recent months, the spy agency has “blocked funds they felt were being used for activities that opposed the government,” said the official, who resigned because of the ministry’s treatment of civil society groups. The official spoke on the condition of anonymity because of the sensitivity of the issue.

“This is not acceptable. Should the security apparatus be monitoring how [foreign] funds are used? How much control should they have over these funds?” the official said. “We have to ask the question: Where does their power stop?”

The official is a rare dissenter inside a bureaucracy that has closed ranks around Sissi.

Human rights workers in Egypt report that they live in fear of arrest, police raids and even violent attacks by security forces, and they say that some activists have received threats in recent months.

In December 2011, security forces stormed the offices of a number of international nonprofits, including two funded by the U.S. government. An Egyptian court later convicted dozens of the organizations’ employees — many in absentia — of illegally receiving foreign funds.

Although there have been no recent dramatic raids, civil society organizations are fearful that they could be targeted at any time.

Ebram Louis is the founder of the Association for the Victims of Abductions and Enforced Disappearances, which monitors kidnappings of members of Egypt’s Coptic Christian minority.

Louis said that the group’s application to register as a nonprofit was rejected because security officials said he was accused of attacking soldiers at a demonstration in Cairo in October 2011. In that incident, military forces killed 27 Coptic Christians who had been marching against sectarian attacks on churches.

Louis said he had to obtain court documents certifying his innocence before submitting another application, which is still pending.

“This is the worst attack on civil society in Egypt’s history,” said Emad Mubarak, executive director of the Association for Free Thought and Expression.

The association, which is partly funded by the Swedish and Dutch governments, has eliminated some of its activities because of the crackdown. Although the association once provided legal aid across the country, its lawyers are now working only in Cairo out of fear for their safety, he said.

“The situation is only going to get worse,” said Emad Mubarak, whose organization is registered as a law association. “We’ve always been threatened, but what we are facing now is on a different level.”

Heba Habib contributed to this report.

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