Gomes was highly critical of the Portuguese government's reluctance to comply with the European Parliament Commission investigation into the CIA flights, leading to tensions with Foreign Minister Luís Amado, a member of her party. She said she had no doubt that illegal flights were frequently permitted during the Durão Barroso (2002–2004) and Santana Lopes (2004–2005) governments, and that "during the Socialist government of José Sócrates, 24 flights which passed through Portuguese territory" are documented. She expressed satisfaction with the opening of the investigation, but emphasized that she had always said a parliamentary inquiry would also be necessary.