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In a statement, the prosecutors said Tariq Saber, Athar Kamel Mohamed Ibrahim, Capt Uhsam Helmi and Maj Magdi Ibrahim Abdelal Sharif were charged with partaking in the "aggravated kidnapping" of Regeni.
Sharif, who is a major in Egypt's general intelligence, is also accused of grievous bodily harm and murder.
Charges were dropped against a fifth security official, Mahmoud Nejm, who had previously been named as a suspect.
Rome's chief prosecutor, Michele Prestipino, described the development as an "extremely important result".
"Prosecutors did everything they could to investigate. We owed it to Giulio's memory," Prestipino said in a hearing before an Italian parliamentary commission on Thursday.
The four men, who will likely be tried in absentia, now have 20 days to submit statements or ask to be heard in the case. Judges will then decide whether to proceed with a trial.
Regeni disappeared in January 2016 in Cairo, where he was carrying out research on Egyptian trades unions, a particularly sensitive political issue in Egypt.
Read more: Bracing for the Biden era, Egypt's Sisi intensifies brazen crackdown on human rights
His badly mutilated body was found in a suburb of the capital a few days later, bearing marks of torture. His mother later said his body had been so badly mutilated she could only recognised her son by the "tip of his nose".
Amid on-off diplomatic spats between Italy and Egypt over the handling of the investigation, multiple theories put forward by Egyptian authorities have been rejected by their Italian counterparts.
Regeni's parents said earlier this month that they had been "subjected to all kinds of hurt and contempt on the part of Egypt, which kidnapped, tortured and killed our son".