Lebanese-born Khaled el-Masri, 48, says he was abducted by CIA operatives under the so-called extraordinary rendition programme while on holiday in Skopje in 2003, and taken to a secret Afghan prison for brutal interrogation.
Initially suspected of having ties to Al-Qaeda, he says he was treated very badly, but later released without charge after five months and sent back to Germany.
A Council of Europe enquiry corroborated details of the case. Masri is suing Macedonia for facilitating his abduction, after Germany and the United States refused to consider his complaints.
At the Strasbourg-based rights court, Masri's lawyers said the Macedonian authorities were to blame for their client's ordeal, that they violated his freedom, treated him inhumanely and then failed to investigate the case.
Macedonia rejects the claims and says the court should not consider Masri's complaint because of issues surrounding the timing of its filing.
Judges did not indicate when they would rule whether Masri's case could proceed.
Rendition flights, in which suspects were transferred covertly to a third country or to US-run detention centres, started after the September 11, 2001 attacks on the United States.