Egypt's National Security forces are allegedly abducting, torturing and "forcibly disappearing" hundreds of citizens in an attempt to wipe out peaceful dissent, Amnesty International has said in a new report.

The human rights association has stated that the clampdown has put at least 34,000 people – by government's own admission – behind bars, including many leaders and senior officials of Muslim Brotherhood, supporters of ousted president Mohammed Morsi and various critics and opponents of the government. It further states that a pattern of abuse has emerged since March 2015 when President Abdel Fattah al-Sisi appointed Major General Magdy Abd el-Ghaffar as Interior Minister.

Philip Luther, director of the Middle East and North Africa Programme at Amnesty International said, "Enforced disappearance has become a key instrument of state policy in Egypt. This report reveals the shocking and ruthless tactics that the Egyptian authorities are prepared to employ in their efforts to terrify protesters and dissidents into silence."

The report also mentions the case of Italian Giulio Regeni, a Cambridge graduate, who was found dead in Cairo. Initially, authorities said he had died as a result of a car accident, but subsequent photographic and autopsy evidence suggested that he had been tortured repeatedly for many days before his death.

Amnesty's Felix Jakens said, "The terrible injuries sustained by Giulio Regeni are similar to those suffered by numerous people interrogated by the Egyptian security forces – his case is just the tip of the iceberg."

Amnesty conducted more than 70 interviews with lawyers, NGOs, family members of victims and included testimonies of 17 of those who survived in the report. One of them includes a 14-year-old student named Mazen Mohammed Abdallah who was taken by police from his home on 30 September 2015, and was subjected to horrendous abuse, including "being repeatedly raped with a wooden stick in order to extract a false 'confession", the document read.

Another child of the same age, Aser Mohammed disappeared for 34 days after being arrested in January. "[He] was beaten, given electric shocks all over his body and suspended from his limbs in order to extract a false 'confession'," the watchdog said.

Luther said that the report exposes not only the brutality faced by the victims, but how National Security Agencies were working in collusion with the judiciary.

The report details that prosecutors based charges on confessions extracted under duress and failed to investigate allegations of torture by ordering medical examinations. In a case where medical examinations were ordered, the lawyers of the victims were not allowed to see the results.

Meanwhile, Egyptian authorities have denied that they were involved in such incidents, but said that certain isolated cases were dealt with responsibly and those who were involved were prosecuted. However, the report says the authorities "did not provide factual evidence to corroborate their denials". It urged the Egyptian president to set up an independent inquiry commission to investigate accusations of torture and enforced disappearances.

Abdelrahman Osama (R) was arrested, aged 17, at dawn on 11 July 2015 by security forces from his home in Cairo while Aser Mohammed (L) was arrested in January 2016 Amnesty