The three men were aged between 27 and 44 and all lived in the coastal town of Savona, Liguria.
They had reportedly been residents in Italy ”for several years” but are suspected of working to spread jihadist propaganda, La Repubblica reported.
The investigation was opened by Liguria's anti-terrorism police after a local girl was mistakenly sent a WhatsApp message from a Moroccan phone number.
The girl raised the alarm when she saw the profile picture of the messages sender, which showed a fighter pointing a machine gun at the camera.
Following the tip off, police in Savona monitored the phone-number, which eventually led them to the group of Moroccan residents.
The men were allegedly working as activists for Isis by spreading jihadist propaganda via social networks.
Since the start of 2015, Italy has expelled some 88 people on terrorism charges. As part the countries no-nonsense approach to dealing with would-be jihadists and terrorist sympathizers most are simply shipped out overnight.
Following recent attacks in Germany and France, Italy's terror alert remains at ‘level two' the highest possible in the absence of a direct attack.
On Monday, bomb scares caused panic on Milan's underground and at a fruit and vegetable market in Ventimiglia, near the French border.