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"The order to abduct Giulio Regeni was given by [police] General Khaled Shalabi, head of criminal police and Giza investigation department," who previously had him followed and his apartment searched, La Repubblica newspaper reported.
La Repubblica also implicated Egypt's leadership in the death of Regeni, saying they were aware of and approved his abduction.
The newspaper said it received the information via email from an anonymous informant in Egypt's intelligence services.
This informant, it said, had also contacted Italian prosecutors and was believed to be credible because he provided details of the torture of Regeni that have not been disclosed so far to the public.
Regeni moved to Cairo in September for research on Egypt's trade union movement. He disappeared on January 25, the fifth anniversary of the 2011 uprising that ousted autocrat Hosny Mubarak.
On February 3, Regeni's body was found on a highway in Giza province on the outskirts of Cairo. Italian officials said it showed clear signs of torture.
La Repubblica reported that Interior Minister Magdy Abdel Ghaffar, National Security chief Mohamed Shaarawi, presidential advisor General Ahmmed Gamal Eddin and the president himself, Abdel-Fattah al-Sissi, were later informed and approved the unlawful detention.
The authorities wanted Regeni to reveal his contacts in the trade union movement, but he refused and was subjected to increasingly brutal questioning, leading to his eventual death at the hands of military intelligence services, it reported.
Italian newspaper La Stampa alleged that Shalabi was the prime suspect, without elaborating.
It suggested that an Egyptian delegation due to meet Italian prosecutors and police on Thursday and Friday in Rome may be ready to pin the murder on him.
Italian Foreign Minister Paolo Gentiloni on Tuesday threatened "immediate and proportional" measures against Egypt if Cairo continued to drag its feet in the investigation.
Both newspapers recalled that a prominent Egyptian rights group, the El Nadeem Centre for the Rehabilitation of the Victims of Violence and Torture, reported in February that Shalabi was one of three police officers handed a one-year suspended jail sentence for torturing to death a man in custody.
The El Nadeem Centre is facing a closure order by Egyptian authorities.