Refugees from the conflict in Syria and women separated from young children figure among those detained in the EU member state, it said in a report.
"By detaining scores of people for months at a time, Cyprus is displaying a chilling lack of compassion and a complete disregard for its international obligations," said Sherif Elsayed-Ali, Amnesty's head of refugee and migrants' rights.
"It is shameful to think that within the EU people who have committed no crime are being held in harsh prison-like conditions for prolonged periods, in some cases for up to 18 months or longer," he said.
The women, longtime residents of Cyprus and married to EU citizens, told Amnesty that the separation had had "devastating effects on their children".
"There can be no excuse for separating a woman who has committed no crime from her children. The treatment of migrants in Cyprus at the moment is degrading and unnecessary," said Elsayed-Ali.
Cyprus ombudsman Eliza Savvidou has also criticised the detention of migrant mothers of young children, while children's rights commissioner Leda Koursoumba has campaigned against separating migrant families.
Amnesty said at least one person at the island's main immigration detention centre, Menoyia, had been held for 22 consecutive months -- in violation of an EU maximum of 18 months -- awaiting deportation.
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