Lithuanian prosecutors on Thursday declined to investigate fresh claims that a Saudi terror suspect was held in an alleged secret CIA jail in the Baltic state.

Last week, two human rights groups said they had lodged a complaint with prosecutors for 45-year-old Mustafa al-Hawsawi, insisting he was imprisoned at an alleged CIA "black site" on Lithuanian soil between 2004 and 2006.

Prosecutors in Vilnius said Thursday the group had failed to provide any evidence of wrongdoing. It also insisted a previous probe had ruled out claims that Al-Qaeda suspects were brought to the EU country.

"The allegations in the complaint cannot be regarded as facts that would raise suspicions about a possible crime by Lithuanian officials," Elena Martinoniene, a spokeswoman for state prosecutors in Vilnius, told AFP Thursday.

The claims of unlawful confinement in alleged CIA secret jails in Lithuania "were nothing new and had been ruled out in a (previous) pre-trial investigation", she said.

The Human Rights Monitoring Institute (HRMI) group in Vilnius told AFP Thursday they would appeal the decision.

Rights groups including Amnesty International have accused Lithuania of foot-dragging on this human rights issue at a particularly sensitive time when it holds the EU's six-month rotating presidency.

Hawsawi, now a Guantanamo inmate, is facing the death penalty for his alleged involvement in the September 11, 2001 attacks on the United States.

He is the second terror suspect alleged to have been illegally held in Lithuania, after top Al-Qaeda operative Abu Zubaydah.

He launched a case with the European Court of Human Rights in 2011.

In December 2009, a Lithuanian parliamentary enquiry identified two sites which it said may have been used as CIA black sites from 2003 to 2006.

But it noted that despite records showing CIA-linked flights landed in Lithuania, it was not possible to say if suspects were actually brought in.

Prosecutors launched a probe but dropped it in 2011 citing insufficient evidence and a statute of limitations.

The Council of Europe has claimed other secret prisons were also set up in Romania and Poland.