Mohammed Fahsi was arrested in Spain in 2006
Spain must end the practice of holding suspects incommunicado, without access to lawyers of their choice and without telling their families, activists say.
Spain's criminal law allows suspects to be held incommunicado for five days.
Amnesty International says it is among the strictest systems in Europe, facilitates torture and breaches international human rights standards.
The Spanish government says its system is no more restrictive than in other countries, and is overseen by judges.
It has previously defended its programme is a necessary counter-terrorism measure.
Amnesty says that under the law, detainees cannot:
- Contact their own lawyer, but can only receive legal assistance from an appointed lawyer
- Consult any lawyer in private
- Have their family informed that they have been detained or where they are held, while foreign nationals cannot inform their embassy
- Choose to be examined by their own doctor, but can only use a state-appointed one
Nicola Duckworth, Amnesty's Europe and Central Asia programme director, said: "Incommunicado detention must be relegated to the past. No other European Union country maintains a detention regime with such severe restrictions on the rights of detainees.
"It is inadmissible that in present day Spain anyone who is arrested for whatever reason should disappear as if in a black hole for days on end. Such lack of transparency can be used as a veil to hide human rights violations."
Spain contested some of the findings in the report. A statement from the interior ministry said "the regime in Spain does not imply more restrictions on rights than those published in the legislation of other EU countries. In some cases our system is less strict."
The statement said detainees had access to a state-appointed lawyer and doctor throughout, and that the process was overseen by a judge.
It said in Spain the maximum period of incommunicado detention was eight days, whereas in Germany it was indefinite.
As early as 2004, the UN special rapporteur on torture, Theo van Boven, issued a report on Spain which said "prolonged incommunicado detention may facilitate the perpetration of torture and could in itself amount to a form of cruel, inhuman or degrading treatment".
Amnesty's new report, Out of the Shadows, cites the case of Moroccan-born Mohammed Fahsi, who was arrested in Spain in 2006 and accused of belonging to a group which sent fighters to Iraq.
His UK-born wife, Khadija Podd, said she was not at home when he was arrested and that the police gave her no information about where he had been taken.
"For days and days it was like he had just vanished," Amnesty quoted her as saying. "Nobody knew where he was. It wasn't until two weeks after he was arrested that I got a phone call from him, in prison. He cried when he spoke to me."
Mr Fahsi said that during his detention he was blindfolded, subjected to threats against his family, and not allowed to rest or sit down for a single minute.
He is due to stand trial in Spain later this month, said an Amnesty spokesman.