The source confirmed reports by Italian news agencies and said Ben-Gvir was being investigated on suspicion of torture and kidnapping of Italian citizens who were among the activists.
If the probe determines charges are warranted, prosecutors could lodge a formal request for trial.
In response to the Italian investigation, Ben-Gvir said in a statement: "I will not shy away from one investigation or another and will continue to stand proudly alongside our fighters."
Israel and Ben-Gvir have faced mounting international criticism after the minister in late May released a video showing detained Gaza activists kneeling with their hands bound after Israel intercepted the aid flotilla in international waters.
Organisers said the 430 activists detained by Israeli police included citizens of Italy, Australia and South Korea.
In a video Ben-Gvir posted on X, officers forced an activist to the ground after she chanted "Free, free Palestine".
The government of Italian Prime Minister Giorgia Meloni called the treatment of the activists "unacceptable" and summoned the Israeli ambassador for an explanation.
Italy subsequently asked the European Union to discuss sanctions against Ben-Gvir, while France has decided to ban Ben-Gvir from its territory.
Last month, 11 Australians detained among the 400 flotilla participants lodged a submission of alleged abuse and mistreatment with the International Criminal Court in The Hague.
Flotilla organisers say they aimed to break Israel's blockade of Gaza by delivering humanitarian assistance, something aid bodies say is still in short supply despite a US-brokered ceasefire between Israel and Hamas in place since October 2025 that includes guarantees of increased aid.
Israel says its naval blockade on Gaza is lawful.
with AAP
