More than 100 children are among thousands of people detained in Egypt in an effort to prevent further protests against the rule of Abdel-Fatah al-Sisi.

At least 3,120 people have been arrested since hundreds of people took to the streets on 20 September, according to the Cairo-based NGO the Egyptian Commission for Rights and Freedoms. Amnesty International said at least 111 children were arrested in the crackdown, “some as young as 11, with several detained on their way home from school”.

Many were held by security services after they were stopped at checkpoints, where officials demanded to see their phones in order to check for “political” material. Local rights groups as well as the government’s own National Council for Human Rights condemned the practice as unconstitutional.

Detainees were added to a single charge sheet, accused of aiding a terrorist group, spreading false information, misuse of social media and participation in unauthorised protests. Amnesty International said this included at least 69 minors aged between 11 and 17. Should the case go to trial, it would be the largest criminal prosecution of protesters in Egyptian history.

Hundreds of people gathered in rare protests against Sisi’s leadership on 20 September, outraged by accusations that the country’s ruling military was squandering public funds on palaces and hotels in a country where 32.5% of people live below the poverty line.

The detentions have touched people from almost every area of public life, from ordinary citizens to journalists and lawyers. The veteran activist Alaa Abd El-Fattah was re-arrested by the Egyptian national security agency from a Cairo police station, where he was forced to sleep as part of his parole. His lawyer, Mohamed El Baqir, was detained when he went to represent him.

Abd El-Fattah’s sister, the activist Sanaa Seif, was also briefly arrested on Sunday for refusing to allow security officials in central Cairo to search her phone.

The arrests even ensnared foreign visitors to Egypt, including two British and American university students who had come to Cairo to study Arabic, and were later accused of espionage.

“We were stopped by a plain-clothes officer who asked to see our phones. I unlocked my phone and handed it to him. He went through every single social media app I had,” said Aaron Boehm, a US citizen. The officer found news articles about the protests on Boehm’s phone, and stopped the pair for over an hour while they read his messages. Boehm was arrested while his friend Ralph Shilcock was interrogated at the hostel where the pair were staying, and pressured into leaving the country.

Facebook Twitter Pinterest Roads to Tahrir Square blocked by security forces to prevent anti-government protests in Cairo. Photograph: Anadolu Agency/Anadolu Agency via Getty Images

Boehm said he was blindfolded and taken to a detention facility. “From this point, I was blindfolded for a total of around 15 hours,” he said, adding that officers interrogated him, demanding to know his motives for being in the country and working with a small organisation teaching English in impoverished neighbourhoods. “At one point they turned me against a wall and yelled that I was ‘in big fucking trouble’,” he said.

“The officer told me he was an Egyptian intelligence officer and that I was accused of espionage. They gave two justifications. Firstly, that my sharing of news articles constituted sharing intelligence with a foreign state, and secondly that my working at an NGO was demonstrative of my intent to undermine the Egyptian regime.”

Boehm was detained for four days. At one point he was taken to a detention facility he believes held 300 others. During his imprisonment he met other foreign nationals including people from the Netherlands, Turkey, Jordan, Eritrea and Yemen, some of whom were later released. He stated that he saw evidence of torture used against detainees, including sticks with blood on them, and heard the screams of other inmates. When asked how many of those he saw in detention were accused of involvement in the protests, Boehm answered: “Every single one.” He was deported on 1 October.

The cybersecurity firm CheckPoint reported this week it had uncovered evidence of a series of cyberattacks targeting critics of the Egyptian regime, including journalists, academics, layers and activists, as well as two opposition figures swept up in the crackdown. The report traced malware, which allowed attackers to track victims as well as read the contents of their phones, to Egyptian government offices.

Facebook Twitter Pinterest Supporters of President Abdel Fattah al-Sisi during a rally in Cairo. Photograph: Mohamed Hossam/EPA

Egypt’s public prosecutor said that fewer than 1,000 people had been detained in relation to the protests, adding that their social media accounts were searched for evidence of “incitement to protesting”. He warned that any online calls to protest would be seen as evidence of “illegal assembly”.

Other Egyptian officials scrambled to respond to the demonstrations. The MP Mostafa Bakri warned that the country should avoid “a war against those who give their opinions”. Ministers attacked the government, accusing it of not doing enough to protect the country’s poor from harsh austerity measures.

Sisi has remained resolute, framing the uprising as fake news perpetrated by foreign powers to destabilise the country. “Throughout the past decades, war has taken different shapes and forms until it now targets the people’s morale, and enters citizens’ houses through new media platforms,” he said.