The London-based group interviewed more than 25 people summoned by the feared National Security Agency in Egypt for its report called "This will only end when you die".
"Activists and human rights defenders said at every summons NSA officers regularly threatened them with arrest and prosecution unless they attended interrogations, and raided the homes of those who failed to appear," Amnesty said.
Most of the 21 men and seven women interviewed described "living in constant fear of being detained by the NSA," said the group.
"As a result, many are too scared to express their opinions or participate in political activities and some have been driven into exile," the rights group said.
The report details how those interrogated, many of them former political detainees, were routinely subjected to "intrusive questioning" with threats of torture against them and their families "if they refused to disclose information".
Human rights defenders interviewed in the report said NSA officers conducted "unauthorised examinations of phones and social media accounts", and the questioning took place without the presence of lawyers.
Egypt's most prominent political prisoner, Alaa Abdel-Fattah, previously told AFP of the strict probation measures he had to observe during a short release between two spells in jail.
Amnesty urged Egypt's President Abdel Fattah al-Sisi, who took power in 2014 after leading the military overthrow of Islamist president Mohamed Morsi the year before, to "put an end to extrajudicial harassment".
Since taking office, Sisi has overseen a sweeping crackdown on dissent, with rights groups estimating that Egypt holds about 60,000 political prisoners.
"I don't want Egyptians to feel that there are human rights violations in Egypt," Sisi said late on Wednesday on a live call-in programme on state TV.
He noted that Egypt would open the "largest prison complex" in the country within a few weeks, following "the US model" of providing "humane" care to detainees.
Earlier this week, Sisi launched a "national strategy" for human rights while taking aim at international rights groups, accusing them of being unaware of the full spectrum of "challenges facing the country".