The interior ministry said 18 police were injured, two of whom were hospitalised, in the protests at the Gevgelija crossing point between Greece and non-EU member Macedonia which came as Macedonian troops began to seal up parts of the border with a 2.5-metre-high fence.
Several police and army vehicles were damaged in the protests, the ministry said in a statement.
Greek news agency Ana reported that Macedonian police fired stun grenades in the migrants' direction.
An AFP photographer earlier saw soldiers using heavy machinery to build a barrier near Gevgelija, on the main road north from the Greek city of Thessaloniki to Macedonia's capital Skopje.
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Gjorgjev said the fence was aimed at ensuring migrants did not try to slip across the frontier undetected, without going through the checkpoint.
Macedonia, a country of around two million people, lies on the main route northwest through Europe trodden by hundreds of thousands of people fleeing war and hardship in the Middle East, Asia and Africa across the Mediterranean to Greece.
Since the summer some central and southeastern European countries, had begun tightening their borders to check the influx -- a trend that has been accelerated by the November 13 shooting and suicide attacks in Paris.
Two of the attackers slipped into Europe through Greece posing as refugees from Syria's civil war, according to French prosecutors.
Since then, countries along the migrant route through the Balkans have tightened restrictions on migrants, allowing entry only to those fleeing war-torn countries such as Syria, Afghanistan and Iraq.
"The border will remain open," Gjorgjev, the spokesman, said yesterday.
"Everyone will be allowed to pass except people who are not from war-affected regions," he told AFP.
The restrictions have sparked protests among frustrated migrants.
On Thursday, around 200 people tried to break through a barbed-wire fence on the Greece-Macedonia border.
Today, a migrant was seriously injured after being electrocuted at the railway station in Idomeni, just across from Gevgelija on the Greek side of the border, police said.
During the past few days, several migrants have taken shelter in parked trains at the station from bad weather.