The boy, a man believed to be his grandfather and a woman believed to be his 52-year-old grandfather's Moroccan girlfriend were found in a burnt-out car in an isolated spot in the Calabria region yesterday.
"How can you kill a small human being like this? This goes beyond any limit," prosecutor Franco Giacomantonio was quoted by Italian media today as saying.
"This is something unprecedented, horrific. In many years of work I think this is the most vicious murder I have ever been faced with," the prosecutor said.
Nunzio Galantino, the bishop of the mountain town of Cassano allo Ionio where the three were from, held a special prayer on Sunday by the car as police took out the skeletal remains -- one of which was in the boot.
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"I am shocked by the level of violence shown by whoever carried out these killings. How can you not hear the cries of a little boy?" Galantino said.
The man is believed to be Salvatore Iannicelli, who was under house arrest for drug trafficking and had gone missing on Saturday. Iannicelli had also been charged in 2012 with kidnapping and sexual violence against a woman.
He lived with his mother in prison for over a year as a baby and once attended a court hearing with her but had since been left in the custody of his grandfather.
The killing was seen as another sign of the end of the historic "honour code" for the local 'Ndrangheta mafia that once spared children, women and the elderly.
The La Stampa newspaper said that since the killing of an elderly local boss in 1975 "the rules were broken and there has been no limit to the barbarity".