Greek police on Monday removed a crowd of stranded migrants blocking a railroad on the border with Macedonia, an official said.
Around 900 people had been blocking the track since Monday, protesting Macedonia's migration policy to allow only Syrian and Iraqi refugees through and stopping all others.
"The operation has begun," said Xanthoula Soupli, mayor of Idomeni, the village on the Greek side of the border where stranded migrants have been piling up.
Only UNHCR workers were allowed to approach the railway border crossing where the protest was staged, while reporters and other aid workers were kept away, Antonis Rigas of the Doctors Without Borders (MSF) organization told Skai TV.
Thousands of people have been massing at the border since Macedonia on Sunday added another filter to its admitting procedure to allow only Syrian and Iraqi refugees through.
The measure stopped Afghans, who had previously been allowed passage along the Balkan migration route from Greece, through Macedonia, Serbia, Croatia and Slovenia to Austria.
Afghan migrants made up the bulk of the crowd that blocked railway traffic at Idomeni, reports said.
Balkan countries in November began stopping all others - mostly from Pakistan, Bangladesh and Africa - regarding them as economic migrants without a chance of receiving asylum in EU countries.
After Austria capped the number of asylum seekers it would take to 80 daily and allow a further 3,200 to pass on to Germany, other Balkan route countries also took steps to limit the influx of migrants.
The Slovenian Parliament late Monday - in a rare display of bipartisan unity - authorized with an overwhelming majority the army to police the border with Croatia.
The measure is intended to suppress trespassing and people smuggling, which has been on the rise in the Balkans since the transit countries began pushing the door shut in recent months.
Filtering war-zone refugees from thousands of economic migrants places Greece under huge pressure.
Unable to stop people from arriving at its Aegean islands from the nearby Turkish coast, Greece worries that it will end up sheltering tens of thousands of stranded migrants.
Only on Tuesday morning, another 1,250 migrants disembarked in Athens from ferries that brought them from the islands, the Greek Coast Guard said.
The authorities are trying to channel the migrants to a collecting centre in a sports arena near the port of Piraeus, but most attempt to continue the journey north on their own, reports say.
Around 1 million people have traversed the Balkan migration route over the past 12 months. Practically all only transited in the hope of securing asylum in Germany and other wealthy countries.