The military's overthrow of President Mohamed Mursi in July after mass protests against him unleashed an "extreme level of political violence", the London-based group told the United Nations Human Rights Council.
"Between 14 and 18 August, at least 1,089 people were killed, many due to the use of excessive, grossly disproportionate and unwarranted lethal force by security forces," said Peter Splinter, Amnesty representative in Geneva.
Egyptian security forces have also failed to prevent or end a wave of sectarian attacks targeting Coptic Christians, he said, referring to attacks on the minority who make up 10 percent of its 85 million people.
"The scale of human rights violations, including of the right to life, the right to fair trial, the right to be free from torture, the right to freedom of expression and assembly, demands an urgent, impartial, independent and full investigation," Splinter said, adding that the results of the inquiry should be made public.
