The report, titled "Egypt: 'Officially, you do not exist': Disappeared and tortured in the name of counter-terrorism," reveals a trend where children as young as 14 have vanished without a trace.
On average, three to four people are seized per day.
Armed security forces led by NSA officers storm the homes of the activists, holding them hostage before taking action. Many of the victims are held for months prior to their release or deportation.
"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," Philip Luther, Director of the Middle East and North Africa Program at Amnesty International, said in a statement .
Anyone who dares to speak out against the government is at risk of being taken. "Enforced disappearance has become a key instrument of state policy in Egypt."
"Counter-terrorism" is being used as an excuse to abduct, interrogate and torture people who challenge the authorities.
Last month, Egyptian authorities stormed into popular TV host Liliane Daoud 's home, hours after her show "Al Soura Al Kamila," which criticized the Egyptian government, was broadcast on ONTV. Daoud, who is Lebanese-British, was detained and deported to Lebanon hours later.
Earlier this year, members of Awlad el-Shawarea were arrested for mocking Egypt's President Abdel Fattah Al-Sisi in a video criticizing the crackdown on anti-Sisi demonstrations and journalists.