"Hundreds of them hit the streets, probably for revenge ... Dozens of police units are gathering to try to control the situation," a police official, who declined to be named, said.
Police responded by firing tear gas at the crowd, evacuating some restaurants in the area, and closing several streets to all traffic.
Hundreds of youths also took to the streets in Thessaloniki, Greece's second largest city, after the news of the shooting was reported.
The protests soon spread to the northern cities of Komotini and Ioannina and the Cretan city of Hania.
Several hours after the incident, Prokopis Pavlopoulos, the interior minister, appologised for the incident on private Mega TV.
"On behalf of the government and the prime minister, I express my sorrow for the incident and especially the death of the young boy," Pavlopoulos said.
"An investigation to clarify the situation has already begun. There will be an exemplary punishment and measures will be taken so that such a thing will not be repeated." He added.
Police sources also said that two police officers were arrested and were being questioned over the incident.