Former Christian militia leader Samir Geagea and militia member Jirjis Khury have been held in "cruel, inhuman and degrading conditions" at the Ministry of Defence Detention Centre (MDDC) in Beirut since 1994, Amnesty said.
Geagea, leader of the Lebanese Forces (LF), was jailed for crimes including assassinating Christian and Muslim leaders during the 1975-1990 civil war. Khury was found guilty of involvement in a 1994 church bombing that killed 11 people.
Amnesty said Khury confessed under torture, that both men were unfairly tried, that the Justice Council that tried them had not investigated the allegations of torture and that both have been held for more than 10 years in solitary confinement.
"Samir Geagea and Jirjis Khury, like scores of other LF members, may have been victims of human rights violations committed in a climate of political repression and intimidation," Amnesty said in a report released on Tuesday.
"The organisation is calling for (the men) to be released or promptly retried, before an ordinary and independent criminal court, in proceedings that conform with international fair trial standards, and for allegations of torture to be investigated."
An Amnesty spokesman told Reuters there had been problems at the MDDC for many years. The report said former detainees had reported mistreatment including being stripped, blindfolded, beaten, having toes crushed and hair pulled out.
"The problem in Lebanon has been there for a long time"
Ordesse Hamad, Amnesty International
"The problem in Lebanon has been there for a long time," Ordesse Hamad, an Amnesty International official said.
"People have been in detention in this place since 1994. So many people were taken there, so many people spoke about torture and ill treatment. And there are also other detention centres."
The London-based rights group said legal problems also went beyond the Justice Council, Lebanon's highest court.
"In this case we are dealing with the highest court in the country but there are also serious flaws in other courts, I think the whole judicial system needs an overhaul," Hamad said.