Amnesty International has suggested that Djibouti was one of the countries where prisoners allegedly abducted and mistreated by the US were held.
The US is accused of transporting suspects to secret jails abroad
The report, based on interviews with former detainees, also links the US practice of "rendition" to the torture or ill-treatment of terror suspects.
Washington has insisted it would never send detainees to places where they would be at risk of torture.
The CIA said it was aware of the report but declined to comment.
The US has a task force based in Djibouti to lead its anti-terror operations across the Horn of Africa.
Yemeni citizen Muhammad al-Assad said US officials, who said they were from the US Federal Bureau of Investigation had questioned him in Djibouti, according to the Amnesty International report titled "Below the radar: Secret flights to torture and 'disappearance'".
He said a picture of the president of Djibouti hung on the wall of the interrogation room.
Mr al-Assad said he spent about two weeks in Djibouti.
The report says Mr al-Assad was arrested in Dar es Salaam in Tanzania, on 26 December 2003 and flown out sometime before dawn the next day.
"Sources in Tanzania have said that he was flown to Djibouti on a small US plane," the report states.
From Djibouti, Mr al-Assad was flown to another location, believed to be in Europe.
He is one of three Yemenis whose cases are highlighted in the report. The other two are believed to have been held in Afghanistan before being transferred to Europe.
The 15,000-word report provides detailed accounts of the experiences of the three men, who claim to have been held in at least four different secret US prisons between October 2003 and May 2005.
The men were allegedly held for 13 months at a so-called "black site", a secret facility believed to be run by the CIA, before they were returned to Yemen, Amnesty said.
In their statements, they gave detailed descriptions of travel times, changing climates and daylight hours which, although not conclusive, Amnesty says suggests they were held in Djibouti, Afghanistan and somewhere in eastern Europe.
The BBC's Rob Watson says although the report is highly critical of the US approach to terrorism suspects, it does not contain any suggestion from the three men that they were tortured by their American captors.
None of the three men was ever charged with any terrorism-related offence.
The US government has said that the transfer of terror suspects is carried out according to US and international law.
However, Amnesty says the CIA is exploiting a loophole that allows private aircraft to land at foreign airports without having to inform local authorities - unlike government or military planes.
The group warned that governments around the world may find themselves "complicit in serious human rights abuses" and urged them to take steps to prevent renditions.