The alleged detentions followed the July 2005 bomb attacks in London, England.
The protest called attention to the claims of 28 Pakistani immigrants who say they were abducted, interrogated and mishandled by unidentified men posing as Greek police.
The protesters said in a statement distributed at the demonstration: "We demand punishment for those guilty of the kidnapping and mistreatment of the 28 immigrants by the secret services."
At least 12 Pakistanis have so far testified that they were held in one unknown location around the capital for varying periods, and questioned about acquaintances in Britain. Some say they were also beaten in the process.
On 11 January, Greece's public order minister denied that his services were involved in illegal interrogations. He admitted that more than 5000 immigrants were monitored after the July attacks in Britain, but in a legal fashion. No links to extremist activities were discovered, he said.