The Former Yugoslav Republic of Macedonia (FYROM) has formally apologised to a German citizen unlawfully seized and handed over to the CIA 14 years ago, following the September 11 attacks in 2001.

FYROM’s Foreign Minister Nikola Dimitrov has written to Khaled El-Masri to express his “sincere apologies and unreserved regrets” for his country’s “improper conduct”, says the human rights group Open Society Foundations. The foreign ministry confirmed the apology to the Associated Press.

After being picked up at FYROM’s border on New Year’s Eve, 2003, El-Masri was held in the capital Skopje for three weeks before being handed over to the CIA and flown to Kabul.

El-Masri said he was held in isolation and mistreated during his detention by FYROM authorities.

He then spent four months at a secret American detention facility in Afghanistan. A later report by the CIA and the US Senate concluded that his interrogators realised early on that he was not a terrorist, but kept him because they thought he was “bad”.

Medical reports noted that El-Masri was bewildered at his detention, and suffered from neglect and “psychological pressures”. At one stage he went on a hunger strike.

When he was released by the CIA in May 2004, El-Masri was flown to Europe and left by the side of the road in Albania.

In December, 2012, the European Court of Human Rights found FYROM in breach of the European Convention of Human Rights and awarded the German €60,000 compensation, which have been paid.

More than five years later, the Open Society Justice Initiative has welcomed the apology. "This certainly goes further than the United States, which continues to refuse to hold anyone at the CIA responsible for this appalling case, or to acknowledge the wrong done to El-Masri, let alone to provide compensation,” said its executive director James Goldston.

El-Masri is being represented by the American Civil Rights Union in a case against the US government. A federal court case was dismissed because it might have revealed “state secrets”, the ACLU says.