The Albanian mother was reported to police by her husband after leaving the family in Barzago in December, Tgcom24 reported.
Two pre-teen girls were left behind along with their father, who tried unsuccessfully to follow his wife and bring their son back to Italy.
Unreleased photos are reported to show the six-year-old being looked after by three other women.
The boy's mother was promised financial benefits by jihadists in Europe to take her son to join Isis, Tgcom said. She had reportedly lived in northern Italy for 20 years.
The investigation into the disappearance of the woman and her son is led by Italy’s special operations police (Ros) and the anti-terrorism wing of the prosecutor’s office in Milan.
News of the woman’s flight follows reports earlier this month that an Italian woman left to join the Isis ranks in Syria.
Maria Giulia Sergio, from Naples, is believed to have left Italy along with her husband in September. She is the only Italian woman know to have joined the extremist group.