The study cited Justice Department figures which indicated that American Indian and Alaska Native women were 2.5 times more likely to be raped or sexually assaulted than women in the United States in general.
The figures said more than one in three Native women would be raped in their lifetime, although that figure may in fact be substantially higher because of a traditional reluctance to report sex crimes.
"Native women are brutalized at an alarming rate, and the United States government, a purported champion of women’s rights, is unfortunately contributing to the problem," said Larry Cox, executive director of Amnesty International USA.
"It is disgraceful that such abuse even exists today. Without immediate action, an already abysmal and outrageous situation for women could spiral even further out of control."
The Amnesty report "Maze of Injustice: The Failure to Protect Indigenous Women From Sexual Violence in the USA" said many rape investigations stalled as officers tried to establish who the investigating authority was.
A dearth of trained Sexual Assault Nurse Examiners at Indian Health Service facilities also meant Native Women do not get timely responses from police and sometimes never received basic forensic medical examinations.
It cited the example of the 2.3 million acre Standing Rock Sioux Reservation spread across North and South Dakota which occasionally has only one police officer on duty to cover the entire region.
To tackle the problem, Amnesty called on Congress to increase funding to the Indian Health Service in order to train and employ more nurses qualified to examine victims of sex attacks.
Amnesty also demanded the federal government provide necessary funding for police forces on Indian reservations and in Alaskan Native villages.