CAIRO (Reuters) - In June 2014, 23-year-old engineering student Mohammed Badawy was expelled from Cairo University.

The university said it ejected him for obstructing the education process, and for rioting and destruction at a protest against President Abdel Fattah al-Sisi's government. Badawy said it was because he protested against the government and supported the Muslim Brotherhood, a political movement that the Egyptian government has banned as a terrorist organisation.

His home was raided by security forces multiple times, he said. Fearing for his life and keen to continue studying, Badawy said he paid people-smugglers to spirit him out of the country.

His reaction was not unusual. The murder of Italian postgraduate student Giulio Regeni has focused new attention on alleged police brutality in Egypt, but nearly a dozen local students have told Reuters they have been targeted over the past three years and regularly face violence and harassment at the hands of security forces.

Regeni, 28, vanished in Cairo on Jan. 25. His body was discovered in a ditch on the outskirts of the Egyptian capital on Feb. 3. It showed signs of extensive torture, which human rights groups say suggests Egyptian police or security forces may have been involved. Egyptian intelligence officials and police sources have told Reuters that on the day Regeni vanished, he was detained by police and then transferred to a compound run by Homeland Security. The police and Interior Ministry deny they were involved and say they never held Regeni.

Rights groups and students say that under Sisi, Egypt's universities have hounded students as a matter of routine, stationing dozens of security forces on campuses, expelling hundreds of students suspected of Islamist leanings, and abusing or torturing many of those they arrest. Some of those arrested admit they support or even belong to the Muslim Brotherhood and have taken part in protests that sometimes turned violent. But often, they say, they were reacting against abuses by the security forces.

Twenty students have been killed by security officials on campuses either while they were protesting or near a protest, according to the Association for Freedom of Thought and Expression, a non-governmental organisation of lawyers and researchers which says it has correspondents in most universities. Reuters was not able to verify these findings.

As well, the association said, more than 790 students have been arrested, mainly for protesting against the government. At least 89 of those were referred to military tribunals. Some have been sentenced to death or life in prison.

Officials from Egypt's two biggest universities say that at least 819 students out of some 700,000 have been expelled from the universities since 2013, the year Sisi ousted the Muslim Brotherhood government. They said the students were expelled for violence and law-breaking. Reuters was unable to verify these figures independently.

In previous years, judges, university officials and veteran lawyers say, the number of expulsions was so small they didn't tally it.

An Interior Ministry official declined to comment about general accusations, saying he could only respond to specific cases. Sisi has described Islamist groups, including the Brotherhood, as existential threats to Egypt, the Arab World and the West.

A senior police official told Reuters that imprisoned students were mostly "accused of joining terrorist organisations and inciting violence." The official also said there has been no torture in Egypt's police stations or any detention facility.

"Any torture incident that takes place is an individual act," he said.

University heads also say there is no campaign against students. The head of one university said his students are offered a second chance if they apologise for protesting and committing violence.

But Mohamed Nagy, a researcher with the Association for Freedom of Thought and Expression, said there was clearly a concerted effort to go after students.

"This era is the worst for students. It never used to happen that hundreds of students used to get expelled from universities. Dealing with students was never that brutal," he said. Nagy himself was arrested on April 25 for taking part in an anti-government protest, his lawyer said. On May 14, a court sentenced him to five years in prison and fined him 100,000 Egyptian pounds ($11,261). Ten days later the court dropped the jail term.

Badawy, the engineering student, said he decided to flee Egypt for fear of ending up in prison. He travelled for five days in the back of a pickup truck through blinding sandstorms and past gun-toting border guards, he said.

A couple of weeks after he arrived in Khartoum, the capital of neighbouring Sudan, he flew to Turkey, where he enrolled in a university in the south. He faces many challenges including financial and language barriers, but he said he and the four other people he fled with feel safer, if unsure of their future.

"The moment we crossed the border and we were safe, we kneeled in prayer," he said during a telephone interview. "Of course, we will be facing a lot of difficulties, but it is still better than what we were living in."

In recent days judges have ruled that tens of students, including Badawy, must be reinstated.

"I am not happy at all," he said from Turkey. Two years after he was expelled, he said, he is angry at the wasted years and his loss of education.

RETURN TO CAMPUS

The crackdown on students started not long after Sisi seized power in July 2013. Millions ofEgyptian protesters had rallied against the rule of democratically elected President Mohamed Mursi of the Muslim Brotherhood. The military, with Sisi at its head, forced Mursi out and took control themselves.

The new government declared the Brotherhood a terrorist organisation, a description the Brotherhood rejects. It also began the fiercest campaign against Islamists in Egypt's modern history. Security forces killed hundreds of Mursi's supporters at Cairo protest camps. Thousands of others, including liberals, were detained.

University campuses have been among the main targets. In February 2014, the government changed the law to give university heads the power to expel students without warning or investigations. That June, about a month after Sisi won an election to become president, he abolished elections for university posts and gave the government back the power to appoint university presidents and faculty deans. Security forces – a ban on their presence on campuses was enforced shortly after the 2011 uprising that led to Mursi's election – were also allowed back.

Cairo University President Gaber Nassar, who helped shape some of the changes, said they were needed to give university leaders the authority "to expel students who take part in violence in a quicker way," and to be able to confront violence "with the sword of law," and "without an investigation."

EXPULSIONS

Being expelled from university is a serious blow in Egypt. A degree is an important badge of status, and once expelled, students have little or no chance of studying elsewhere. In January 2014, the Supreme Council of Universities, a government body, banned private universities from accepting students who had been expelled.

Many students who have been expelled say Egypt doesn't let them leave to pursue an education abroad either, because they have criminal records – either in connection with the expulsions or for protesting against the government. Young men are not allowed to leave the country without having done military service or being formally exempted. That forces some, like Badawy, to flee secretly.

Most of the students now in jail were studying at Al-Azhar University and Cairo University, the senior police official said.

Al-Azhar alone has expelled 419 students in the past two years, mostly for protesting against the government, according to spokesman Hossam Shaker. He said the expulsions were fair and not part of any government campaign.

"All means are given to the students to prove their innocence. The university is not looking to incriminate the students," the spokesman said, adding that some were expelled for violating a law that effectively bans protests.

One 20-year-old who used to study at Al-Azhar said he was kicked out after leading protests against the government. He said he struck a dean who had called him a "son of a bitch" for protesting in support of the Muslim Brotherhood and had tried to stop him from taking his final exam. After torching two police cars, the student said, he ended up at a police station and a state security building. The student did not identify the dean, and Reuters was unable to seek his comment.

The student, who described himself as a Muslim Brotherhood sympathiser, said he was subjected to electric shocks, hanged for days by his feet and hands, and sexually assaulted several times with a stick.

"I felt that I was breathing my last breath. I was almost dead," he said. "My body was so weak. They used to give me a break from torture for nearly two hours a day."

After 22 days, he said, he was sent to solitary confinement, where he stayed for two months. Reuters was not able to independently verify the details of his account.

Once freed, he said he made the 30-hour drive from Cairo to Port Sudan. Passengers sat on the back of pickup trucks and clung to sticks rammed vertically among the luggage for support. His truck raced towards the border.

"I was about to fall off," he said by phone from Khartoum. "I was too tired to hold on from the intensity of the heat.

"I am dreaming of the day where I can go back. I think of revenge every day, but I am trying to be patient."

"HUMILIATION"

Cairo University President Nassar said the system offers second chances. Several times, he has issued an open invitation to students expelled from his university to come and meet him, in the presence of their parents, and apologise. If they promise not to protest again, he said, they are reinstated.

Last year, at least 91 students took him up on the offer, he said. "I'm aware that (for) those who genuinely belong to the Muslim Brotherhood, it will be very difficult for them to accept such an initiative."

Reuters spoke to three of those who attended such meetings and were reinstated after apologising. They said they still live in fear of arrest or another expulsion.

Two brothers – Ahmed and Abdel Rahman – said that despite being reinstated they have left the country to finish their education in Malaysia. "He who expels me once for no good reason and without an investigation, can expel me again," said Ahmed, 22, an engineering student.

A 21-year-old engineering student said he had been expelled and reinstated twice after he attended meetings with Nassar. The second time he was expelled, in 2014, the university said it was because he had rioted, thrown Molotov cocktails at security forces, terrorised citizens and obstructed the education process. He said he had done none of those things and now lived away from home because he feared arrest.

All three students said the meetings with Nassar were humiliating. They were not allowed to speak, ask questions or sit down during the hour-long session, they said.

Nassar said he had long discussions with students. "I sat with them for more than two hours, we talked, we agreed and disagreed. We don't hold them accountable for their affiliation."

From Turkey, engineering student Badawy said he would never apologise.

"Apologising means that I am admitting that I have done the things that they have accused me of. But I haven't. Also, criminal charges don't drop when I apologise," he said. "This is severe humiliation that I can't accept."

FRUSTRATED

Brotherhood supporter Gihad Fayez, 23, was in her fourth year in the faculty of commerce at Al-Azhar University's El-Zagazig branch northeast of Cairo when she learned she had been kicked out. She spotted her name on a list of expelled students posted on a university fence.

The notice said that following an investigation, she and eight other students had been found guilty of  "obstructing the education process" and protesting. She rejects those charges and said that in her case, she was not summoned for an interview until a month after being expelled. She believes she was targeted because she filmed anti-government protests, shared the films online, and exposed alleged abuse by the security forces.

She applied to multiple private universities but was turned down – she believes because of the 2014 law. "I was frustrated. I felt that I wanted to learn but the country doesn't want me to learn," she said.

"Two days after my expulsion I felt that my whole life had stopped. I was crying. I felt sorry for myself. Is this what I deserve for defending my friends?"

She appealed, filing a complaint with the administrative court a month after her expulsion in December 2014. But her case has been delayed.

LED INTO VIOLENCE?

At an administrative court complex in Giza on Cairo's outskirts in March, a judge flanked by two deputies sat near a table heaving with hundreds of documents.

The papers detailed the defence arguments of expelled students and staff as well as other cases. The judge barely glanced at the papers.

There was a series of short hearings during which each lawyer spoke for less than a minute. Then the judge announced the court would adjourn.

Later, Hamed Al-Moraly, vice chairman of the state council and a member of the  six-person judicial panel, blamed the delay on the universities, saying they had failed to present the necessary papers. There had been a problem with the interpretation of the law, he added. And the court was overwhelmed by the number of cases coming in.

Omar Dahy, the head of the court, told Reuters that the expulsions were far more numerous than before the Arab Spring. "The reasons behind the expulsions (nowadays) weren't there during Mubarak's time," Dahy said. "There wasn't a revolution during Mubarak's time."   

While Muslim Brotherhood protests have faded, Western diplomats and security officials believe young members of the group are carrying out attacks on police.

Some former students are talking about full-fledged jihad, says lawyer Abdel Aziz Youssef, who spent four months in jail with students late last year. A small but growing number of youngEgyptians are vulnerable to Islamic State's radical ideology: "The number of students who see peaceful means of expression as useless is on the rise," he said.

(Additional reporting by Mohamed Abdellah; Edited by Mike Georgy and Sara Ledwith)