The Open Society Justice Initiative said some have allowed Central Intelligence Agency planes to use their airspace. Others have gone much further, allowing secret prisons in their territory or cooperating with the CIA in capturing and detaining suspected terrorists.
The report, based on public sources, names 136 people detained under the programs.
"By apparently co-opting as many as 54 foreign governments in these illegal operations, the U.S. undermined longstanding human rights protections enshrined in international law, including, in particular, the norm against torture," said Amrit Singh, the group's senior legal officer. "Leaving aside the damage to its moral standing, the U.S. has exposed itself to liability and censure worldwide."
A number of cases brought by former detainees are now pending in the European Court of Human Rights. The court ruled in December that Macedonia violated the rights of a detainee named Khaled el-Masri by cooperating with the CIA in his detention.
In Italy, both CIA officers and officers with Italian security services were prosecuted.
Other countries named in the report include Australia, Iceland, Morocco and Thailand.
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