Some suspects were held uncharged for weeks
The human rights group claimed that many of 1,200 non-US nationals jailed since the terrorist attacks were held in "harshly punitive conditions" which appeared "excessive".
"We are concerned that the Immigration Service is being used to hold people on flimsy evidence, pending broad criminal probes, without due safeguards," it said.
Detainees were routinely shackled for court appearances, said the report, which was compiled from numerous interviews with lawyers, detainees, and relatives and from visits to two prisons.
"The government's treatment of these individuals is simply unacceptable and is a violation of international law," Amnesty International Executive Director William Schulz said in a statement.
Secrecy
The report says 36 prisoners were held without charges for more than a month under a post-11 September rule which allows the Immigration and Naturalization Service to detain people for an "undefined period" in "extraordinary circumstances".
"Why am I imprisoned? Why in solitary confinement? And why under maximum security measures?", one detainee quoted in the report wrote after more than three months in the Metropolitan Detention Centre in New York.
Most of the detainees are thought to be men from Muslim or Middle Eastern countries.
But the US Justice Department has refused to release the names and other details of those held in connection with immigration violations.
US Attorney-General John Ashcroft has said the information is "too sensitive" for the public domain.
Lawsuit
The Justice Department said last month that 327 people were in detention - either on immigration violations or because they were being investigated for "possible terrorist connections".
Amnesty International and other human rights groups have filed a lawsuit seeking the disclosure of detailed information on those detainees and people already released.
The organisation said this was necessary to ensure detainees were treated humanely, in accordance with international law, and were not deported to a country where they could face serious human rights abuses.
Mr Ashcroft has said his department has carefully crafted moves to combat terrorism to ensure they do not infringe the rights enshrined in the country's constitution.