"I can confirm the Italian nationality of the victim but not his identity, the corpse was burnt," a foreign ministry spokesman said, adding that identity documents had been found with the body.
The victim has been identified by the Italian media as Roberto Gianfalla, from Palermo.
Nosy Be lies just off the northern tip of the vast Indian Ocean island.
"Rioters launched a manhunt and killed the Europeans," in the early hours of Thursday morning after a missing eight-year-old was reportedly found dead, gendarmerie commander Guy Bobin Randriamaro said.
Local police commissioner Honoya Tilahizandry said the men "were killed and burnt on Ambatoloaka beach", a popular palm-fringed stand ringed by bars and hotels.
Gory pictures taken after the lynching showed a mound of ash, wood and iron bars, with a torso and pair of charred legs the only recognisable remains.
"They suspected the two foreigners of being behind the murder and trafficking human organs," said the gendarmerie's Randriamaro.
The two men "confessed under torture to having trafficked organs", he added. Hours later in a nearby suburb, a Malagasy was also killed, as mobs of hundreds of men roamed the streets setting fires.
The victim was reportedly dragged from a vehicle and his body thrown onto a fire.
In Paris, foreign ministry spokesman Philippe Lalliot said "two foreigners have died and we have confirmation that at least one of them is French".
The Frenchman had a 60-day tourism visa and his passport indicated he was a frequent visitor to the island nation.
Ramanamahafahy said an ministerial delegation had arrived on the island for a meeting with local leaders before visiting the family of the dead child as well as of the "two people shot dead."
Until now authorities had confirmed only one person had been shot dead when paramilitary police opened fire on protesters on Wednesday night.