"No legal or policy reforms were implemented to eradicate torture under either the SCAF [Supreme Council of Armed Forces] or President Morsi's administration," the organization said.
"Torture and other ill-treatment continued and security forces acted with impunity," the human rights group said.
The comments were in Amnesty International's annual report on Egypt, covering 2012, Ahram Online reported Friday.
AI quoted a non-governmental Egyptian group, which said 88 people were subjected to torture during Morsi's first 100 days in power.
The report also criticized the government's use of military trials for civilians and the possible legalization of discrimination against minorities, Ahram Online said.
"The new constitution did not explicitly prohibit discrimination on the basis of race, potentially affecting minorities such as Nubians," the report said.