In what the rights group described as “arbitrary arrests” and “illegal” mass expulsions, the migrants were detained in the Algiers area and Blida, 50 kilometres (30 miles) to the southwest.
They were then placed on buses and taken 2,000 kilometres south to Tamanrasset, it said.
They were then “abandoned” on the Nigerien side of the border between the two countries.
At least 100 others, dropped on the Algerian side of the frontier, had to walk for six hours in the desert, it said.
It said migrants of several nationalities were also deported via the Malian border.
Amnesty accused Algeria of “ethnically profiling” migrants and failing to check if they had official permission to stay in the country.
It said some of those deported since September 22 had valid visas, and that the deportations “did not respect the guarantees of due process”.
Heba Morayef, Amnesty’s North Africa research director, said Algeria “must urgently put an end to these illegal arrests and expulsions”.
The group said those deported, from various sub-Saharan African countries, included 300 minors — some of them unaccompanied.
NGOs say about 100,000 Sub-Saharan Africans live in Algeria, many in precarious circumstances.
In September, Algeria repatriated 1,000 undocumented Nigeriens.
In June, social media users sparked controversy with a hashtag calling for “no Africans in Algeria”.
Prime Minister Ahmed Ouyahia later accused “illegal aliens” of bringing “crime, drugs and other plagues” to the country.
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