Hundreds of rioters fought pitched battles with police in the Greek cities Athens and Thessaloniki following the fatal shooting of a 16-year-old boy Saturday night.

Witnesses said the shooting occurred about 9:00 p.m. local time, when a small group of youths attacked a police patrol car in Athens. A police officer fired three shots, hitting the teenager in the chest. Witness accounts diverge widely about what happened.

Several hours after the incident, police issued a statement saying the patrol car, with two officers inside, was attacked by a group of 30 stone-throwing youths while patrolling the central Athens district Exarchia.

The statement said the two officers left their car to confront the rioters.

"The two [police officers] maintain that they were attacked again and responded, with one firing a stun grenade and the other, by shooting three times, resulting in the fatal wounding of the minor," the statement said.

Two Greek TV stations said the youth was rushed to a hospital but died upon arrival.

The two officers and the local precinct commander have been suspended pending an investigation, the statement said.

"The government expresses its profound regret over this incident. An inquiry on the circumstances of the death has already begun and, if the policemen are found to have been derelict in their duty, the punishment will be exemplary," Interior Minister Prokopis Pavlopoulos said in a statement.

The news enraged hundreds of youths in the area, who began attacking other police cars with stones and firebombs. Police responded by firing tear gas at the crowd, evacuating some restaurants in the area and closing several streets to all traffic.

A few hours after the rioting began, the youths appeared to divide into at least three separate groups and there was a lull in the fighting.

At least one teenager was arrested but no casualties were reported among the rioters or police.

Shortly after midnight, rioting resumed with increased intensity, with some protesters marching through the city centre and others fighting police outside the National Technical University of Athens nearby. Police made heavy use of tear gas and rioters responded with stones, firebombs and other projectiles.

In the northern city Thessaloniki, dozens of youths attacked a police precinct in the city centre and several others blockaded a central city artery, near the Thessaloniki University campus.

Calls were posted on websites, including the Independent Media Centre, for more people to join the protests in Greece's two main cities, as well as Iraklio on Crete.

Earlier Saturday, hundreds of migrants waiting to submit asylum applications rioted in downtown Athens for an hour, setting fire to garbage bins and attacking passing cars.

Protesters said the riot began when one man fell into a nearby canal after authorities told the crowd no more applications could be submitted.

It was not immediately clear how the man fell into the canal but police said he was injured and taken by ambulance to a hospital.