The migrants, including women and children, forced their way past a Greek police cordon onto a rail track and tried to break through a barbed wire fence into Macedonia, shouting "open the borders."
Macedonian police stopped them by firing tear gas grenades.
Macedonia on February 21 entirely closed its border to Afghans, stranding hundreds in Greece, and introduced more stringent document checks for Syrians and Iraqis seeking to cross its territory en route to northern and western Europe.
This came as French authorities began bulldozing the southern half of the "Jungle" migrant camp in the northern port city of Calais on Monday.
Two bulldozers and around 20 workers began destroying dozens of makeshift shacks, with 30 police cars and two anti-riot vans stationed nearby.
Four million refugees have fled Syria for the relative safety of neighbouring countries, according to the United Nations, with more than one million in Lebanon - swelling the population by 25 percent.
Greece is the main entry point for migrants to the EU, with most coming over the Aegean Sea to Turkey via the Greek islands.
Athens faces growing pressure to stop "waving through" migrants to the rest of Europe, but it has criticised the response of the EU.
|The United Nations says Europe is backing into an even greater refugee crisis by tightening border restrictions|
Greek migration minister, Yannis Mouzalas, in particular criticised Balkan countries that held talks in Austria at a meeting excluding Greece for agreeing border measures that would affect his country.
Many European nations have adopted a raft of restrictive measures since the beginning of the year as they seek to stem the influx.
Since the beginning of the year more than 110,000 migrants and refugees have arrived in Europe after crossing the Mediterranean, adding to the more than one million people that landed on the continent in 2015, according to the International Organisation for Migration.
But the United Nations says Europe is backing into an even greater refugee crisis by tightening border restrictions on the hundreds of thousands fleeing conflicts elsewhere.
UN High Commissioner for Refugees Filippo Grandi visited the port and registration centres
"I am very worried about the news we are getting about the increasing closures of the European borders along the Balkans route," Grandi said, adding that the situation would create further chaos and increase the burden on Greece.
He emphasised the need to further promote the option of relocation, saying the scheme would significantly reduce the numbers moving to Austria, Germany and Sweden and ease the pressure on Greece.