A former CIA officer who was accused of taking part in an illegal counter-terrorism programme said she is facing imminent extradition to Italy from Portugal after a high court in Lisbon rejected a last-minute legal appeal.

Sabrina de Sousa, a 60-year-old former CIA officer who was convicted in absentia in Italy in 2009, faces a four-year prison term for her alleged role in the kidnapping of a radical Egyptian cleric named Abu Omar, who was grabbed off the street in Milan by CIA officials in 2003 and sent to Egypt, where he was imprisoned, interrogated and allegedly tortured.

The extradition of De Sousa and her possible imprisonment in Italy would mark the first time that any CIA officer connected to the highly classified and controversial Bush-era extraordinary rendition programme faced jail.

In an interview with the Guardian over Skype, De Sousa said she had not been told when precisely she would be sent to Italy but said she hoped officials would not knock on her door without warning. She said it was unclear what would happen once she arrived in Italy, where she is to formally be read her sentence. Italian officials have not stated whether that means she will then be sent to prison automatically or whether she could appeal.

“It is such an uncertain situation, it really is. I just have to have a certain degree of faith, I suppose. It is a little unnerving,” De Sousa said. “I actually feel more for my family, I just explained to them that it has to be done. It is an enormous injustice.”

According to De Sousa, the constitutional court in Portugal is due to formally hand down its rejection of her final appeal to a lower court, which in turn is expected to contact Portuguese police, setting off a formal process between Italian and Portuguese officials.

The Italian justice ministry, which is responsible for the case, did not immediately comment.

The development marks an extraordinary turn of events in a case that had essentially been dormant for years, even after a dogged and independent Italian prosecutor in Milan, Armando Spataro, pursued the Abu Omar case, exposing the classified programme to the world. The prosecutor’s investigation led to the conviction in absentia of De Sousa and more than 20 other American officials. While De Sousa was convicted under her real name, she told the Guardian that most of the others were convicted under their aliases, and are therefore free to travel the world without fear of being detained.

The case was thrown back into the spotlight late last year after De Sousa, who has dual US and Portuguese citizenship, made the risky decision to leave the safe confines of the US and travel to Portugal, where she was still subject to an EU arrest warrant. De Sousa was detained in an airport in Lisbon in October as she was trying to leave the EU to travel to India to visit her mother.

Her detention set off a chain of events in Portugal, where she has lost several appeals to try to stop her extradition based on her claims that the legal proceeding against her was unfair and that there was no evidence against her.

The radical Egyptian cleric Abu Omar was grabbed off the street in Milan in 2003. Photograph: Nasser Nasser/AP

De Sousa, a vocal critic of the CIA and US government, has said she is a low-level and innocent scapegoat who has been sacrificed by the US government while high-ranking officials who executed the extraordinary rendition programme have received impunity.

There have been no public signs of support for her case by the US government. A spokesman for the US embassy in Rome declined to comment.

Italy’s president, Sergio Mattarella, granted partial pardons to two other defendants in the Abu Omar case late last year, but has so far not responded to a request for clemency by De Sousa.

The former CIA officer, who was working in Italy under diplomatic cover, has said she took part in early stage discussions of the extraordinary rendition programme in general but not specifically about Abu Omar. She has denied any involvement in his kidnapping.

De Sousa, who is Catholic, told the Guardian that she has written a letter to Pope Francis, urging him to denounce the rendition programme employed by the CIA after the 11 September terror attacks against the US.

The De Sousa case been criticised by some conservative media outlets, including the Wall Street Journal editorial page, which accused the Obama administration of abandoning one of its operatives and sending a “demoralising message to all who serve in the shadows, even as the war on terror enters a dangerous new phase”.

Abu Omar, who now lives in Egypt, has also come to De Sousa’s defence, saying he believed she ought to be pardoned and that she had helped to expose the “injustices” in his case.

In an interview with McClatchey in 2013, De Sousa alleged that the former CIA station chief in Rome, Jeffrey Castelli, had exaggerated the threat Abu Omar posed to win approval for the rendition in Washington, which she claimed was approved by then CIA director George Tenet.

The Abu Omar case helped to expose the role US allies, including Italy, played in the rendition programme. The Guardian recently reported that British involvement in the clandestine programme provoked an unprecedented row between the UK’s domestic and foreign intelligence services, MI5 and MI6, at the height of the war on terror.

