The report into violent racism shows that at least 28 people were killed and 366 were assaulted in 2005.
This year there have already been a number of high-profile cases, including the death of a Senegalese student.
Amnesty condemns discrimination by the authorities and a failure to properly record or investigate racist crimes.
The Amnesty report, entitled "Russian Federation: Violent racism out of control", includes examples of police and prosecutors routinely classifying murders and serious assaults by skinhead extremists as lesser crimes of "hooliganism".
Amnesty International UK Director Kate Allen said racist killings and violent attacks against foreigners, visible ethnic minorities and anti-racist campaigners in Russia were out of control.
"Some Russian authorities are turning a blind eye," she said. "Instead of seeing only 'hooliganism' in vicious organised attacks on students from African, south-east Asian countries and non-Slavic Russians from Chechnya, Russia's police and prosecutors need to tackle head-on the growing scourge of violent racism in Russia."
She said President Vladimir Putin's government should adopt a comprehensive "plan of action" to combat racism and anti-Semitism.
Cases highlighted in the Amnesty report include the killing of nine-year-old Tajik girl Khursheda Sultonov.
She was attacked with other members of her family in St Petersburg in February 2004 by a gang. Khursheda was stabbed nine times in the chest, stomach and arms and died at the scene.
Another victim was Vu Anh Tuan, a 20-year-old Vietnamese student, stabbed to death in October 2004 by a gang of 18 skinheads near a metro station in St Petersburg.
Dmitri Krayukhin, head of anti-racist organisation United Europe, told Amnesty he had received threats to "cut off your head".
He has repeatedly been denied protection from the authorities in Orel, western Russia.
The report also heard from members of the Roma community who have stopped travelling into St Petersburg city centre, having been the victims of attacks.
Russian citizens and foreigners living in the big cities have led demonstrations against the attacks and the authorities' failure to tackle the problem.